Methods of diagnosing inflammatory bowel disease through RNASET2

ABSTRACT

Described herein are methods of diagnosing inflammatory bowel disease, including but not limited to Crohn&#39;s Disease (CD), Ulcerative Colitis (UC), and/or Medically Refractive Ulcerative Colitis (MR-UC), using RNA-SET2, TL1A and/or IFN-Y. The methods may comprise treating inflammatory bowel disease by administering a therapeutically effective amount of a therapeutic agent to a subject. Described further herein are processes for patient identification and/or stratification.

CROSS-REFERENCE TO RELATED APPLICATIONS

This application is a U.S. National Phase of International ApplicationNo. PCT/US2017/023082 filed Mar. 17, 2017, which claims the benefit ofU.S. Provisional Ser. Nos. 62/457,048 filed Feb. 9, 2017 and 62/309,817filed Mar. 17, 2016, all of which are incorporated herein in theirentirety.

STATEMENT REGARDING FEDERALLY SPONSORED RESEARCH OR DEVELOPMENT

This invention was made with government support under Grant Nos.DK043211, DK046763, DK062413, HS021747, AI067068, DE023798, DK084554,RR033176 and TR000124 awarded by the National Institutes of Health. Thegovernment has certain rights in the invention.

FIELD OF INVENTION

The invention relates to inflammatory bowel disease and RNASET2 as abiomarker for disease severity and targeting anti-TL1A therapy.

BACKGROUND

All publications herein are incorporated by reference to the same extentas if each individual publication or patent application was specificallyand individually indicated to be incorporated by reference. Thefollowing description includes information that may be useful inunderstanding the present invention. It is not an admission that any ofthe information provided herein is prior art or relevant to thepresently claimed invention, or that any publication specifically orimplicitly referenced is prior art.

Inflammatory bowel disease (IBD) has two common forms, Crohn's disease(CD) and ulcerative colitis (UC), which are chronic, relapsinginflammatory disorders of the gastrointestinal tract. Genetic factorsplay an important role in IBD pathogenesis, as evidenced by theincreased rates of IBD in Ashkenazi Jews, familial aggregation of IBD,and increased concordance for IBD in monozygotic compared to dizygotictwin pairs (S. Vermeire, P. Rutgeerts, Genes Immun 6, 637 (2005)).Moreover, genetic analyses have linked IBD to specific genetic variants.CD and UC are thought to be related disorders that share some geneticsusceptibility loci but differ at others.

IBD is generally believed to be triggered in genetically susceptibleindividuals by an inappropriate immune response to the commensal flora.The high clinical heterogeneity and genetic complexity of CD and UCsuggest that the underlying biological pathways driving disease almostcertainly differ in subgroups of patients. Thus, the development ofearly and targeted therapeutics requires subgroup stratification andprognostic biomarker identification, particularly in predicting anoverall mild, compared to severe, disease course. Although 201 IBDsusceptibility loci have been identified, little is known regardingtheir functional significance. Genetic variation in TNFSF15 isassociated with CD in multiple populations, and the protein it encodes,TL1A, is a key mediator of mucosal inflammation. TL1A expression isup-regulated in inflamed regions of the intestine in both CD and UC. InIBD patients, elevated TL1A levels correlate with TNFSF15 genotype anddisease severity. CD patients with elevated serum/tissue levels of TL1Ahave increased risk of developing fibrosis/stricturing disease behavior.In vitro, TL1A synergizes with interleukin 12 (IL-12) and interleukin 18(IL-18) (12/18), leading to rapid enhancement of IFN-γ production,another key mediator of mucosal inflammation.

Therefore, there remains a need in the art for methods of diagnosing andidentifying patients for treatment with IBD, CD, UC and/or MR-UC.

BRIEF DESCRIPTION OF THE FIGURES

Exemplary embodiments are illustrated in referenced figures. It isintended that the embodiments and figures disclosed herein are to beconsidered illustrative rather than restrictive.

FIG. 1 depicts RNASET2 eQTL microarray in uninvolved small intestine, inaccordance with various embodiments of the invention.

FIG. 2 shows that the RNASET2 major allele is associated with decreasedexpression of RNASET2 in sigmoid colon and rectum of CD patients, inaccordance with various embodiments of the invention.

FIG. 3 shows that the RNASET2 major allele is associated with decreasedexpression of RNASET2 in sigmoid colon and rectum of UC patients, inaccordance with various embodiments of the invention.

FIG. 4 shows that the RNASET2 risk allele is associated with decreasedexpression of RNASET2 in inflamed large bowel in CD and UC patients, inaccordance with various embodiments of the invention. Similar resultswere observed for rs1819333.

FIG. 5 shows that the RNASET2 major allele is associated with decreasedRNASET2 expression in small bowel from CD surgeries, in accordance withvarious embodiments of the invention.

FIG. 6 depicts RNASET2 eQTL in EBV Transformed B Cell Lines, inaccordance with various embodiments of the invention. The major alleleis associated with lower levels of RNASET2 mRNA expression in EBVtransformed B cell lines.

FIG. 7 depicts RNASET2 expression following IL-12, IL-18, and/or TL1Aand treatment, in accordance with various embodiments of the invention.

FIGS. 8A-8C depict RNASET2 expression in CD patients, in accordance withvarious embodiments of the invention. A) RNASET2 expression in patientswith none or 1 multiple disease flares per year. B) RNASET2 expressionfollowing TL1A treatment in patients who were medically refractiverequiring surgical intervention for disease management or no surgery. C)RNASET2 expression based upon disease flares per year in 32 CD patients,encompassing additional data samples.

FIG. 9 shows a decreased expression of RNASET2 in IBD patients withRNASET2 risk alleles, in accordance with various embodiments of theinvention.

FIG. 10 depicts RNASET2 methylation versus GWAS p values in CD and UCpatients, in accordance with various embodiments of the invention.

FIG. 11 depicts the eQTL of RNASET2 in refractory IBD, in accordancewith various embodiments of the invention. RNASET2 SNPs (rs2149085,rs1819333 and rs9355610) from CD3+ peripheral T cells from 11 CD and 10UC patients requiring surgical intervention for disease management,using an Illumina expression array.

FIG. 12 depicts the eQTL of RNASET2 in CD small bowel (ileal) surgicalresection of 85 CD patients using an Agilent expression array, inaccordance with various embodiments of the invention.

FIGS. 13A-13D depict the mQTL of RNASET2 in refractory IBD, inaccordance with various embodiments of the invention. A) mQTL of RNASET2in refractory IBD and B) normal or mild disease patients. C) mQTL(cg25258033) of CD3+ peripheral T cells from 20 CD patients withrefractory disease requiring surgical intervention for diseasemanagement and D) 16 patients who were responsive to IBD therapeuticsand 9 normal controls, encompassing additional data samples.

FIGS. 14A-14B depict the mapping of eQTL and mQTL across RNASET2 inpatients with refractory or mild disease, in accordance with variousembodiments of the invention. A) eQTL and mQTL across RNASET2 inpatients with refractory or mild disease. B) eQTL and mQTL calculatedusing CD3+ T cells from both the periphery and mucosal compartments frompatients with refractory or mild disease (including normal patients),encompassing additional data samples.

FIG. 15 depicts sorting and IFNγ expression of CD4+ T cells stimulatedwith IL-12, IL-18 and/or TL1A, in accordance with various embodiments ofthe invention. Histograms of side scatter vs. IFN-γ for CD4+ T cellsstimulated with recombinant human IL-12 (500 pg/ml) and IL-18 (50 ng/ml)and TL1A (100 ng/ml) for 8 h from 4 donor (D1-4).

FIG. 16 depicts a dendrogram of hierarchical clustering using centeredcorrelation and average linkage, in accordance with various embodimentsof the invention.

FIG. 17 depicts a class prediction analysis classifying theIFNγ-secreting and non-secreting subgroups based on expression level, inaccordance with various embodiments of the invention. Heatmap of 764predictor genes.

FIG. 18 depicts a proportion of genes differentially expressed that wasincreased in GWAS versus other regions, in accordance with variousembodiments of the invention.

FIG. 19 depicts 183 transcribed IBD associated SNP regions in the Tcells, in accordance with various embodiments of the invention.

FIG. 20 depicts a volcano plot of the class predictor GWAS transcriptsof IBD risk predictor genes, in accordance with various embodiments ofthe invention.

FIGS. 21A-21B show that silencing RNASET2 enhances IFN-γ secretion, inaccordance with various embodiments of the invention. A) Inhibition ofRNASET2 by RNASET2 siRNA. B) Effect of RNASET2 silencing on IFN-γsecretion. Enhanced IFN-γ expression in cellos transfected with RNASET2siRNA compared to control scrambled siRNA.

FIG. 22 demonstrates the inverse correlation of IFN-γ and RNASET2expression in accordance with various embodiments of the invention.

FIG. 23 demonstrates a negative correlation of RNASET2 methylation andexpression in CD3⁺ T cells (cg25258033, located 1.4 kb within the firstintron) in 21 IBD patients, in accordance with various embodiments ofthe invention.

FIGS. 24A-24D depict correlation of RNASET2 and TNFSF15 expression inCD3+ T cells from patients with refractory disease requiring surgicalintervention for disease management, using RNA-seq, in accordance withvarious embodiments of the invention. A) Correlation of RNASET2 versusTL1A in refractory CD. B) Correlation of RNASET2 and TNFSF15 expressionin CD3+ peripheral T cells from 38 CD patients, C) depicts data from 100CD patients and D) depicts combined data from 138 patients.

FIG. 25 depicts the correlation expression of RNASET2 versus A) PU.1 andB) ELF1, in accordance with various embodiments of the invention. Therisk SNP rs2149092 C/T (SEQ ID NO: 2) abolishes the IRF4, PU.1, andELF-1 binding site. C— non-risk and T=risk allele.

FIG. 26 depicts correlation of expression and methylation located within100 kb of the RNASET2 transcriptional start site in 21 IBD patients, inaccordance with various embodiments of the invention.

FIG. 27 depicts IFN-γ expression of IFN-γ producing and non-producinglevels in CD4+ T cells, in accordance with various embodiments of theinvention.

FIG. 28 depicts the correlation of GWAS p values with eQTL p values overthe RNASET2 locus, in accordance with various embodiments of theinvention. GWAS p values are based upon data from 18729 CD and 34897controls. eQTL p values are based upon genotyping and RNA-seq basedexpression of RNASET2 for 71 CD patients with refractory disease,requiring surgical intervention for disease management.

FIG. 29 depicts the effect of RNASET2 silencing on IFN-γ secretion, inaccordance with various embodiments of the invention. Inhibition ofRNASET2 expression by RNASET2-specific siRNA was greater than 50% in allexperiments.

FIG. 30 depicts an association of decreased expression of RNASET2 withASCA Sero-positivity, in accordance with various embodiments of theinvention.

FIG. 31 depicts an association of a decreased expression of RNASET2 withpenetrating disease, in accordance with various embodiments of theinvention. Expression of RNASET2 by RNA-seq for 71 CD patients basedupon Montreal disease classification (B1, B2, and B3).

FIG. 32 depicts that patients with RNASET2 disease associated SNPsexhibited a shorter time to reoperation, in accordance with variousembodiments of the invention. Time between surgeries based upon carriagefor IBD risk SNP rs9355610 (SEQ ID NO: 3) for 154 CD patients whounderwent multiple surgeries.

FIG. 33 depicts that the rs2149092 SNP (SEQ ID NO: 2) Alters DNA Shape.

FIG. 34 depicts the correlation of RNASET2 versus Ets1 expression, inaccordance with various embodiments of the invention.

FIG. 35 depicts that the rs2149092 SNP (SEQ ID NO: 2) distorts DNA shapeat the Ets1 binding site.

FIGS. 36A-36C depict identification of potential regulatory function ofRNASET2 disease associated variant rs2149092 (SEQ ID NO: 2) theprospective regulatory role of RNASET2 variant rs2149092 (C-non-riskallele/T-risk allele), in accordance with various embodiments of theinvention. A) Predicted disruption of rs2149092 C to T variation in thebinding motifs for ETS and IRF4 transcription factors. Central ETS inthe variant motif is underlined. B) CHIP-seq and histone modificationprofiles for ETS1, IRF4 and SPI1 transcription factor binding andhistone H3K4me1 and H3K4ac aligned with the genomic sequence surroundingrs2149092 variant. C) Correlation of expression of RNASET2 and multipleETS and JUN transcription factors in CD3+ peripheral T cells from 108 CDpatients requiring surgical intervention for disease management, usingRNA-seq.

FIGS. 37A-37G depict the effect of RNASET2 silencing on IFN-γ secretionand cellular aggregation, in accordance with various embodiments of theinvention. A) Silencing of RNASET2 expression by RNASET2 or control (NC)siRNA. B) Effect of RNASET2 silencing on IFN-γ secretion. Panels A and Bare representative of 6 out of 7 experiments (FIG. 29) with similarresults. C) CD4+ T cells were either not treated (UT) or D) stimulatedwith TL1A for 24 hours. Intracellular IFN-γ staining and cellularaggregations were measured by flow cytometry. Cells were gated on IFN-γsecreting and non-secreting populations (left panels) and then usingpropidium iodide (PI) analyzed for single and aggregate cell fractions(histograms, right panels). The first peak in each histogram correspondsto single cells (black bracket) and the remaining peaks to cellularaggregates (gray bracket). Representative of 4 experiments. E)Proportion of single cells and cellular aggregates in IFN-γ secreting(IFN-γ+) and non-secreting (IFN-γ−) populations following TL1Astimulation. F) Fold increase in number of IFN-γ secreting cells(Average of 4 experiments). G) CD4+ T cells were pretreated with controlIgG or LFA1 blocking Ab (aLFA1) prior to TL1A stimulation. Overall pvalue for LFA1 mediated blocking of IFN-γ secretion, measured by ELISA,was 0.047.

FIG. 38 depicts in accordance with various embodiments of the invention,the association of RNASET2 disease risk variant SNPs at the time ofsurgery with therapeutic failure of thiopurine or anti-TNF therapy, ANCAsero-positivity and an increased length of intestinal resection (datasummarized in Table 18).

FIG. 39 depicts in accordance with various embodiments of the invention,the association of RNASET2 disease risk variant SNPs with diseaserecurrence in 38 patients who were not receiving postoperativeprophylaxis. Post-operative endoscopies were performed and classified byRutgeerts score. (data summarized in Table 18).

FIG. 40 depicts tissue-specific functional annotation of RNASET2 locus.Heatmap of H3K4me3, H3K4me1 and RNAseq data from REMC.

FIG. 41 depicts the correlation of RNASET2 expression and multiple ETSand IRF4 transcription factors in CD3+ peripheral T cells from 108 CDpatients with refractory disease, using RNA-seq.

FIG. 42 depicts in accordance with various embodiments of the invention,a heat-map illustrating protein expression of indicated genes in CD4+ Tcells relative to untreated cells following silencing with control (NC)or RNASET2 siRNA. Results are from 4 healthy donors. The right columndepicts differential gene expression in IFN-γ secreting compared tonon-secreting CD4+ T cells.

FIG. 43 depicts in accordance with various embodiments of the invention,clinical disease parameters associated with level of ICAM1 expression(measured by RNA-seq) for 71 CD patients based upon IgG ASCAsero-positivity (left panel) or pre-op therapeutic failure of anti-TNF(middle panel) or thiopurine (right panel).

DESCRIPTION OF THE INVENTION

All references cited herein are incorporated by reference in theirentirety as though fully set forth. The sequences related to RNASET2 arealso incorporated by reference in their entirety as though fully setforth via the rs number disclosed. Unless defined otherwise, technicaland scientific terms used herein have the same meaning as commonlyunderstood by one of ordinary skill in the art to which this inventionbelongs. Singleton et al., Dictionary of Microbiology and MolecularBiology 3rd ed., Revised, J. Wiley & Sons (New York, N.Y. 2006); andSambrook et al., Molecular Cloning: A Laboratory Manual 4^(th) ed., ColdSpring Harbor Laboratory Press (Cold Spring Harbor, N.Y. 2012), provideone skilled in the art with a general guide to many of the terms used inthe present application. For references on how to prepare antibodies,see D. Lane, Antibodies: A Laboratory Manual 2^(nd) ed. (Cold SpringHarbor Press, Cold Spring Harbor N.Y., 2013); Kohler and Milstein,(1976) Eur. J. Immunol. 6: 511; Queen et al. U.S. Pat. No. 5,585,089;Riechmann et al., Nature 332: 323 (1988); Bird, Science 242:423-42(1988); Tomlinson I. and Holliger P. (2000) Methods Enzymol, 326,461-479; Holliger P. (2005) Nat. Biotechnol. September; 23(9):1126-36).

One skilled in the art will recognize many methods and materials similaror equivalent to those described herein, which could be used in thepractice of the present invention. Indeed, the present invention is inno way limited to the methods and materials described. For purposes ofthe present invention, the following terms are defined below.

Non-limiting examples of “Biological sample” as used herein means anybiological material from which nucleic acids and/or proteins can beobtained. As non-limiting examples, the term encompasses whole blood,peripheral blood, plasma, serum, saliva, mucus, urine, semen, lymph,fecal extract, cheek swab, cells or other bodily fluid or tissue,including but not limited to tissue obtained through surgical biopsy orsurgical resection. Alternatively, a sample can be obtained throughprimary patient derived cell lines, or archived patient samples in theform of preserved samples, or fresh frozen samples.

“Treatment” and “treating” as used herein refer to both therapeutictreatment and prophylactic or preventative measures, wherein the objectis to prevent or slow down (lessen) the targeted pathologic condition,prevent the pathologic condition, pursue or obtain good overallsurvival, or lower the chances of the individual developing thecondition even if the treatment is ultimately unsuccessful. Those inneed of treatment include those already with the condition as well asthose prone to have the condition or those in whom the condition is tobe prevented.

“SNP” as used herein means single nucleotide polymorphism.

“Risk variant” as used herein refers to an allele, whose presence isassociated with an increase in susceptibility to an inflammatory boweldisease, including but not limited to Crohn's Disease, UlcerativeColitis and Medically Refractory-Ulcerative Colitis, relative to anindividual who does not have the risk variant.

“IBD”, “CD”, “UC” and “MR-UC” as used herein refer to Inflammatory BowelDisease, Crohn's Disease, Ulcerative Colitis and Medically RefractiveUlcerative Colitis, respectively.

As used herein, “IBD” includes “CD”, “UC” and/or “MR-UC”.

As used herein, “ANCA” means anti-neutrophil cytoplasmic antibodies.

As used herein, “OmpC” means outer membrane protein C.

As used herein, “eQTL” means expression quantitative trait loci.

As used herein, “mQTL” means methylation quantitative trait loci.

Non-limiting examples of RNASET2 SNPs are rs1819333, rs2149092,rs9355610, rs2149085, rs1410295 and rs9366093.

Described herein are methods of diagnosing inflammatory bowel diseaseusing RNASET2, TL1A and/or IFN-γ as a biomarker of disease severity in apatient population and selecting the patient population for anti-TL1Atherapy. Further described are methods of treating these patientpopulations.

RNASET2 (ribonuclease T2) encodes an extracellular RNase and is the onlymember of the human Rh/T2/S family of acid ribonucleases (acidhydrolyses), which are only active in acidic pH. The optimal activity ofRNASET2 is at pH 5 and it has a preferential cleavage of poly-A andpoly-U. It contains two regions with catalytic function and demonstratesa cleavage preference near adenylic acid followed by guanylic acid.Three isoforms have been detected for RNASET2, the 27KD, 31KD and 36KDisoforms. The 27KD and 31KD isoforms are thought to result fromproteolytic cleavage of the 36KD isoform. All three isoforms areglycosylated. Subcellular fractionation reveals that full length RNASET2is located in the endoplasmic reticulum and the two smaller RNASET2proteolytic products are located in the lysosome fraction. RNASET2 ishighly conserved among the phyla, from viruses to humans, suggesting animportant evolutionary function.

TL1A (TNFSF15) is a tumor necrosis factor family member expressedprimarily on activated cells of the immune system, such as monocytes,macrophages, and dendritic cells, following stimulation by immunecomplexes or through interaction with enteric microorganisms. TL1Aexpression is enhanced in inflammatory bowel disease and higher TL1Alevels are associated with disease severity. Genome-Wide AssociationStudies (GWAS) have identified TNFSF15 SNPs to be associated with IBD.Studies have shown that neutralizing TL1A antibodies attenuate colitisin murine colitis models, while constitutive TL1A expression depicts aworsened murine ileo-cecal inflammation and intestinal fibrostenosis.

IFN-γ plays a key role in the generation and perpetuation of mucosalinflammation in IBD. TL1A augments IL-12/IL-18-mediated IFN-γ secretionin PB T cells.

The inventors identify RNASET2, an IBD susceptibility gene, as acomponent of TL1A-mediated enhancement of IFN-γ production. Moreover,functional variants of RNASET2 are associated with a more ‘severe’ CDphenotype characterized by one or more disease flares andstricturing/penetrating disease behavior. Without being bound to anyparticular theory, the inventor believes that RNASET2 serves as atherapeutic biomarker associated with severe disease pathobiology andallows for the identification of a patient population most likely tobenefit from therapy targeted to the TL1A-driven inflammatory pathway.The TNFSF15 disease-associated variants are correlated with increasedand sustained expression of TL1A. TNFSF15 has been identified andconfirmed in GWAS as an IBD-associated gene and is believed to play arole in modulating the location and severity of intestinal inflammation,as well as development of stricturing disease. Transgenic mice withconstitutive expression of TL1A developed intestinal inflammation alongwith ileal and colonic fibrosis, which was reversed by anti-TL1Atreatment. In UC, there is a strong association between development of amedically refractory disease and the TL1A locus. Although TL1A is animportant pro-inflammatory cytokine associated with IBD pathogenesis,the molecular pathways underlying enhanced cytokine secretion andinflammation were poorly understood. Described herein, the inventorsinvestigated the TL1A-dependent molecular triggers that induce cytokineexpression, particularly IFN-γ, in T cells. This approach identifieddown-modulation of RNASET2 as a component of TL1A-mediated enhancementof IFN-γ production.

The inventors demonstrate a functional association of RNASET2 diseaserisk SNPs with decreased expression and hyper-methylation in T cellsisolated from CD patients, as well as, an association with clinicalparameters suggestive of complicated/resistant disease behavior andrapid recurrence of disease. The inventors show the regulatory potentialfor ETS TF in modulating RNASET2 expression and the involvement ofhomotypic T cell aggregation via ICAM1 as a component of RNASET2mediated up-regulation of IFN-γ production. The data distinguish RNASET2as a potential therapeutic biomarker and identify unique pathways foradditional therapeutic modulation within a defined IBD population.

The inventors found that, in IBD patients, there was a significantinverse correlation between the expression of RNASET2 and TNFSF15. Inaddition, the inventors demonstrate a functional association between DNAhyper-methylation and decreased expression of RNASET2.

The inventors found that there was significant eQTL overlap with RNASET2IBD risk alleles identified through GWAS in samples isolated from theperipheral T cells and small bowel surgical resections. SignificantRNASET2 eQTL (rs429083) has been described in a recent report thatmeasured autoimmune associated risk variants in whole thymic tissuesamples. This SNP demonstrated the most significant eQTL in the data, aswell. Moreover, the study provides clinically relevant evidence thatdecreased expression levels of RNASET2 were correlated in CD patientswith clinical parameters suggestive of complicated and resistantdisease. Notably, CD patients carrying the RNASET2 disease risk SNPsdisplayed an increase in development of stricturing/penetrating diseasebehavior. RNASET2 expression was significantly lower in T cells isolatedfrom CD patients exhibiting one or more disease flares per year.Similarly, RNASET2 expression is decreased in small bowel mucosalsamples, as well as, in peripheral samples from medically refractory CDpatients (9 out of 11 which were non-responsive to anti-TNF therapy),requiring surgical intervention for disease management. Consistent withthe finding, a recent study reported significant RNASET2 eQTL in wholeblood from patients resistant to anti-TNF therapy. Moreover, RNASET2disease-associated SNPs correlated with therapeutic failure of anti-TNFtherapy, and intestinal resection of >40 cm clinical characteristic ofoverall disease severity. In patients with a history of multipleresections, RNASET2 disease risk SNP was associated with a faster timeto reoperation. Likewise, RNASET2 disease associated SNPs wereassociated in patients with endoscopic recurrence characterized by amore severe (>2) Rutgeerts score, which without being bound to anyparticular theory, can be predictive for early clinical recurrence andneed for reoperation.

The transcriptional regulatory regions and binding factors modulatingRNASET2 expression are likewise poorly defined. The majority of diseaseassociated variants identified by GWAS reside within regulatorynon-coding regions corresponding to promoters or enhancer sequences.Without being bound to any particular theory, studies suggest thatalteration in transcriptional regulation via disruption of transcriptionfactor binding sites may play a role in the disease process. In thepresent study the inventors utilized TF motif analysis to prioritize andidentify from the large number of variants demonstrating eQTL and mQTL aprospective regulatory SNP. The rs2149092 disease associated SNP altersthe conserved ETS consensus binding sequence and likely disrupts bindingof multiple overlapping TF binding sites including IRF4, SPI1 and ELF1.Moreover, there is a strong positive correlation between the levels ofRNASET2 expression and ETS and JUN TF family members. Interestingly,IRF4, SPI1 and ELF1 have been implicated in T cell development and IRF4and ELF1 have been associated by GWAS with IBD. Without being bound toany particular theory, these data support a functional role forrs2049092 as a modulator of TF-DNA interactions and set the stage forfuture studies to determine the mechanistic pathways by which TL1Aattenuates expression of RNASET2 in disease.

In the present study the inventors describe a functional relationshipbetween RNASET2 and the cell adhesion molecule, ICAM1. Enhanced IFN-γsecretion in response to TL1A was accompanied by a decrease in RNASET2expression on the one hand and an increase in ICAM1 levels on the other.TL1A mediated IFN-γ secretion was inhibited by Ab blockade of theICAM1-LFA1 interaction. Although ICAM1-LFA1 engagement is classicallydefined as occurring between endothelial and T cells, these interactionshave more recently been shown to play a critical role in mediatinghomotypic cellular aggregation of activated T cells. Homotypic T-Taggregates have been shown to promote synaptic-based cytokine deliveryof IFN-γ and IL2 from one T cell to another, resulting in IL-2 receptorligation and subsequent STATS phosphorylation. The inventors demonstratethat enhanced cellular aggregation is a hallmark of IFN-γ producingcells and TL1A-stimulation increases the number and size of the cellularaggregates. Without being bound to any particular theory, these findingssuggest that RNASET2 may act through the integrin signaling pathway tomodulate downstream IFN-γ secretion.

In conclusion, the inventors identified a novel functional andbiological relationship between two IBD susceptibility genes, TNFSF15and RNASET2. The inventors provide evidence that decreased RNASET2expression is functionally implicated in both the TL1A drivenpro-inflammatory cytokine production by activated T cells andfunctionally associated with the RNASET2 IBD susceptibility variants.Likewise, the present study demonstrates an association betweendecreased RNASET2 expression and a more severe form of IBD inflammation,which without wishing to be bound by any particular theory, we believeunderlie disease pathology triggered by TL1A mediated pathways.Decreased expression and altered epigenetic DNA methylation of RNASET2characterize a subset of IBD patients with a more severe diseasephenotype. The inventors demonstrate a functional association of RNASET2disease risk SNPs with decreased expression and hyper-methylation in Tcells isolated from CD patients, as well as, an association withclinical parameters suggestive of complicated/resistant disease behaviorand rapid recurrence of disease. The inventors show the regulatorypotential for ETS TF in modulating RNASET2 expression and theinvolvement of homotypic T cell aggregation via ICAM1 as a component ofRNASET2 mediated upregulation of IFN-γ production. The data distinguishRNASET2 as a potential therapeutic biomarker and identify uniquepathways for additional therapeutic modulation within a defined IBDpopulation. Thus, RNASET2 expression serves as a novel disease biomarkerof a more severe form of inflammation identifying a patient populationnot responsive to current treatment strategies, whom may benefit fromalternate RNASET2 mediated therapeutic approaches.

As disclosed herein, the inventors have identified RNASET2 associatedSNPs in an IBD patient cohort. The inventors have identified RNASET2associated SNPs in a CD patient cohort. The inventors have identifiedRNASET2 associated SNPs in a UC patient cohort. The inventors haveidentified RNASET2 associated SNPs in a MR-UC patient cohort. The SNPswere associated with disease location, disease behavior and need forsurgery. The inventors have further identified RNASET2 as a biomarkerfor disease severity and associated RNASET2 risk SNPs in an IBD patientcohort. RNASET2 has been identified as a biomarker for disease severityand associated RNASET2 risk SNPs in a CD patient cohort. RNASET2 hasbeen identified as a biomarker for disease severity and associatedRNASET2 risk SNPs in a UC patient cohort. RNASET2 has been identified asa biomarker for disease severity and associated RNASET2 risk SNPs in aMR-UC patient cohort. In addition, the inventors demonstrate acorrelation between RNASET2, TL1A expression and IFN-γ secretion.

The present invention is based, at least in part, on these findings. Thepresent invention addresses the need in the art for methods ofdiagnosing patients with IBD and identifying patients in need oftreatment, using RNASET2, TL1A and/or IFN-γ. The invention furtherprovides a process for patient identification and/or stratification.

Diagnosis

Various embodiments of the present invention provide for a method ofdiagnosing inflammatory bowel disease (IBD) in a subject, comprising:obtaining a sample from the subject; subjecting the sample to an assayadapted to determine the presence or absence of one or more riskvariants at the RNASET2 gene; and diagnosing IBD in the subject based onthe presence of one or more risk variants at the RNASET2 gene. In someembodiments, inflammatory bowel disease is Crohn's disease, ulcerativecolitis or medically refractive ulcerative colitis. In variousembodiments, the one or more risk variants at the RNASET2 gene isrs1819333, rs2149092, rs9355610, rs2149085, rs1410295 or rs9366093. Invarious embodiments, the subject is diagnosed with IBD if 2, 3, 4, 5 or6 RNASET2 risk variants as described herein are present. In variousembodiments, the risk allele for rs2149085 is the T allele. In variousother embodiments, the RNASET2 risk variants are the RNASET2 riskvariant rs429083 and an RNASET2 risk variant selected from the groupconsisting of rs1819333, rs2149092, rs9355610, rs2149085, rs1410295,rs9366093, and combinations thereof. In various other embodiments, theRNASET2 risk variants is one or more of the RNASET2 risk variants inTables 2, 3, 4, 5, 6, 7, 8, 9, 10, and 13 and an RNASET2 risk variantselected from the group consisting of rs1819333, rs2149092, rs9355610,rs2149085, rs1410295, rs9366093, and combinations thereof. In variousother embodiments, the one or more risk variants at the RNASET2 gene isrs1819333, rs2149092, rs9355610 or rs2149085. In various embodiments,the subject is diagnosed with IBD if 2, 3, or 4, RNASET2 risk variantsrs1819333, rs2149092, rs9355610 or rs2149085, as described herein arepresent. In other embodiments, the presence of a greater number of riskvariants in the sample indicates that the subject is in greater need oftreatment. In some embodiments, the detection of RNASET2 risk variantsis indicative of the need for treatment in the subject. In yet otherembodiments, the subject is identified as needing anti-TL1A therapy. Invarious embodiments, the subject diagnosed with IBD demonstratestherapeutic failure of thiopurine and anti-TNF therapy. In various otherembodiments, the subject diagnosed with IBD is determined to needsurgical intervention. In some embodiments, the surgical intervention isintestinal resection.

TABLE 1 RNASET2 risk variants SNP SEQ ID NO: rs1819333 1 rs2149092 2rs9355610 3 rs2149085 4 rs1410295 5 rs9366093 6

In other embodiments, the method of diagnosing inflammatory boweldisease (IBD) in a subject described herein comprises determining theexpression level of RNASET2, TL1A and/or IFN-γ. In some embodiments, asubject with decreased RNASET2, and/or increased TL1A and/or IFN-γlevels is diagnosed with IBD. In various embodiments, inflammatory boweldisease is Crohn's disease. In various embodiments, inflammatory boweldisease is ulcerative colitis. In various embodiments, inflammatorybowel disease is medically refractive ulcerative colitis. In variousembodiments, inflammatory bowel disease is a CD patient who requiredsurgical intervention for disease management. In yet other embodiments,a subject with decreased RNASET2, and/or increased TL1A and/or IFN-γlevels is identified as a subject in need of a treatment that increasesRNASET2, and/or decreases TL1A and/or IFN-γ. In other embodiments, thesubject is identified as needing anti-TL1A therapy. In yet otherembodiments, the subject is identified as needing a treatment thatcauses an increase in RNASET2. In certain other embodiments, the subjectis identified as needing a treatment that causes a decrease in IFN-γand/or TL1A.

In various embodiments, the detection of RNASET2 risk variants and/orRNASET2, TL1A and/or IFN-γ expression levels can be accomplished byanalyzing nucleic acids of a biological sample from the subject. Avariety of apparatuses and/or methods, including, without limitation,polymerase chain reaction based analysis, sequence analysis andelectrophoretic analysis can be used to detect RNASET2 risk variants.The expression levels of RNASET2, TL1A and/or IFN-γ can be detectedusing a variety of apparatuses and/or methods, including, withoutlimitation, quantitative PCR, northern blot and microarrays. As usedherein, the term “nucleic acid” means a polynucleotide such as a singleor double-stranded DNA or RNA molecule including, for example, genomicDNA, cDNA and mRNA. The term nucleic acid encompasses nucleic acidmolecules of both natural and synthetic origin as well as molecules oflinear, circular or branched configuration representing either the senseor antisense strand, or both, of a native nucleic acid molecule.

In various other embodiments, determining the expression level ofRNASET2, TL1A and/or IFN-γ can be accomplished by analyzing the proteinsof a biological sample from the subject. A variety of apparatuses and/ormethods, including, without limitation, ELISA, immunohistochemistry, andwestern blot can be used to detect RNASET2, TL1A and/or IFN-γ expressionlevels.

Various embodiments of the present invention also provide for a methodof diagnosing medically refractive ulcerative colitis (MR-UC),comprising: obtaining a sample from the subject; subjecting the sampleto an assay adapted to determine the presence or absence of one or morerisk variants at the RNASET2; and diagnosing MR-UC in the subject basedon the presence of one or more risk variants at the RNASET2 gene. Invarious embodiments, the one or more risk variants at the RNASET2 geneare rs1819333, rs2149092, rs9355610, rs2149085, rs1410295 or rs9366093.In various embodiments, the risk allele for rs2149085 is the T allele.In various other embodiments, the RNASET2 risk variants are the RNASET2risk variant rs429083 and an RNASET2 risk variant selected from thegroup consisting of rs1819333, rs2149092, rs9355610, rs2149085,rs1410295, rs9366093, and combinations thereof. In various otherembodiments, the RNASET2 risk variants is one or more of the RNASET2risk variants in Tables 2, 3, 4, 5, 6, 7, 8, 9, 10, and 13 and anRNASET2 risk variant selected from the group consisting of rs1819333,rs2149092, rs9355610, rs2149085, rs1410295, rs9366093, and combinationsthereof. In various other embodiments, the one or more risk variants atthe RNASET2 gene is rs1819333, rs2149092, rs9355610 or rs2149085. Invarious embodiments, the subject is diagnosed with IBD if 2, 3, or 4,RNASET2 risk variants rs1819333, rs2149092, rs9355610 or rs2149085 asdescribed herein are present.

In various embodiments, the subject diagnosed with MR-UC demonstratestherapeutic failure of thiopurine and anti-TNF therapy. In various otherembodiments, the subject diagnosed with MR-UC is determined to needsurgical intervention. In some embodiments, the surgical intervention isintestinal resection. In various embodiments, the subject diagnosed withMR-UC is determined to need RNASET2 mediated therapy, such as but notlimited to recombinant RNASET2 and anti-ICAM1. In various embodiments,the RNASET2 mediated therapy is an antibody or small molecule thattargets genes that are upstream and/or downstream of RNASET2.

In various other embodiments, the methods further comprise determiningthe level of methylation of RNASET2, and diagnosing IBD in a subject whohas an increase in RNASET2 methylation. In other embodiments, the levelof RNASET2 methylation is determined to diagnose a subject with MR-UC.In some embodiments, the subject is identified as needing a treatmentthat causes a decrease in RNASET2 methylation. In other embodiments, thesubject is identified as needing an anti-TL1A therapy.

Various embodiments of the present invention provide for the treatmentof subjects diagnosed with MR-UC. MR-UC subjects are refractory tocurrent conventional medical therapy used, such as anti-TNF therapy,thiopurine therapy, corticosteroids and cyclosporine. In variousembodiments, the subjects diagnosed with MR-UC are treated withnon-conventional treatments, such as, but not limited to treatments thatmimics, modulates and/or targets RNASET2, TL1A and/or IFN-γ. In variousembodiments, treatments that mimics, modulates and/or targets RNASET2,TL1A and/or IFN-γ can comprise antibodies and or silencingoligonucleotides. In various embodiments, the subject diagnosed withMR-UC is determined to need RNASET2 mediated therapy, such as but notlimited to recombinant RNASET2 and anti-ICAM1. In various embodiments,the RNASET2 mediated therapy is an antibody or small molecule thattargets genes that are upstream and/or downstream of RNASET2.

In various embodiments, the subject is identified as needing a treatmentthat mimics, RNASET2, TL1A and/or IFN-γ. In other embodiments, thesubject is identified as needing a treatment that modulates RNASET2,TL1A and/or IFN-γ. In some other embodiments, the subject is identifiedas needing a treatment that targets RNASET2, TL1A and/or IFN-γ. In yetother embodiments, the subject is identified as needing a treatment thatmimics, modulates and/or targets RNASET2, TL1A and/or IFN-γ. In variousembodiments, treatments that mimics, modulates and/or targets RNASET2,TL1A and/or IFN-γ can comprise antibodies and or silencingoligonucleotides. In various embodiments, the disease is IBD. In variousembodiments, the disease is CD. In various embodiments, the disease isUC. In various embodiments, the disease is MR-UC. In variousembodiments, the subject diagnosed is a CD patients who requiredsurgical intervention for disease management.

In various embodiments, the presence of one or more risk variants at theRNASET2 gene is associated with decreased expression of RNASET2. Inother embodiments, the presence of one or more risk variants at theRNASET2 gene is associated with decreased expression of RNASET2 inperipheral and mucosal tissues. In some other embodiments, the presenceof one or more risk variants at the RNASET2 gene is associated with DNAhypermethylation in patients requiring surgical intervention for diseasemanagement. In yet other embodiments, the presence of one or more riskvariants at the RNASET2 gene is associated with therapeutic failure ofthiopurine and/or anti-TNF therapy. In some other embodiments, thepresence of one or more risk variants at the RNASET2 gene is associatedwith ANCA sero-positivity. In various other embodiments, the presence ofone or more risk variants at the RNASET2 gene is associated withincreased overall length of intestinal resection.

Subject Identification and/or Stratification

Various embodiments of the present invention provide for a process ofidentifying a subject with inflammatory bowel disease for treatment,comprising: determining the expression level of RNASET2, TL1A and/orIFN-γ; and identifying the subject in need of treatment as a subjectwith decreased RNASET2, and/or increased TL1A and/or IFN-γ levels. Invarious embodiments, the inflammatory bowel disease is Crohn's disease.In various embodiments, the inflammatory bowel disease is ulcerativecolitis. In various embodiments, the inflammatory bowel disease ismedically refractive ulcerative colitis. In various other embodiments,the subject is identified as needing a treatment that causes an increasein RNASET2. In yet other embodiments, the subject is identified asneeding a treatment that causes a decrease in TL1A and/or IFN-γ. Incertain embodiments, the subject is identified as needing anti-TL1Atherapy. In some embodiments, the subject is identified as needing atreatment that mimics, modulates and/or targets RNASET2, TL1A and/orIFN-γ. In various embodiments, treatments that mimics, modulates and/ortargets RNASET2, TL1A and/or IFN-γ can comprise antibodies and orsilencing oligonucleotides.

“Patient Risk Stratification” as used herein means the process ofseparating subjects into risk groups in need of treatment.

Various embodiments of the present invention provide for a process ofpatient risk stratification to identify a subject in need of treatment,relative to a healthy individual. In various embodiments, the subject isstratified based on the detection of RNASET2, TL1A and/or IFN-γ in abiological sample from the subject. In some embodiments, a decrease inRNASET2 is indicative of a patient having IBD, in need of treatment. Insome embodiments, a decrease in RNASET2 is indicative of a patienthaving CD, in need of treatment. In some embodiments, the patient is aCD patient who requires surgical intervention for disease management. Insome embodiments, a decrease in RNASET2 is indicative of a patienthaving UC, in need of treatment. In some embodiments, a decrease inRNASET2 is indicative of a patient having MR-UC in need of treatment. Invarious other embodiments, an increase in TL1A and/or IFN-γ isindicative of a patient having IBD, in need of treatment. In variousother embodiments, an increase in TL1A and/or IFN-γ is indicative of apatient having CD, in need of treatment. In various other embodiments,an increase in TL1A and/or IFN-γ is indicative of a patient having UC,in need of treatment. In various other embodiments, an increase in TL1Aand/or IFN-γ is indicative of a patient having MR-UC, in need oftreatment. In certain other embodiments, a decrease in RNASET2, anincrease in TL1A, and an increase in IFN-γ is indicative of a subjecthaving IBD, in need of treatment. In certain other embodiments, adecrease in RNASET2, an increase in TL1A, and an increase in IFN-γ isindicative of a subject having CD, in need of treatment. In certainother embodiments, a decrease in RNASET2, an increase in TL1A, and anincrease in IFN-γ is indicative of a subject having UC, in need oftreatment. In certain other embodiments, a decrease in RNASET2, anincrease in TL1A, and an increase in IFN-γ is indicative of a subjecthaving MR-UC, in need of treatment. In various embodiments, detection ofthe genes provides a guide for the treatment of the subject. In certainembodiments, the subject is identified as needing a treatment thatmimics, modulates and/or targets RNASET2, TL1A and/or IFN-γ. In variousembodiments, treatments that mimics, modulates and/or targets RNASET2,TL1A and/or IFN-γ can comprise antibodies and or silencingoligonucleotides. In various other embodiments, the process of patientrisk stratification to identify a subject in need of treatment isrelative to a healthy individual who has been previously treated. Invarious other embodiments, the process of patient risk stratification toidentify a subject in need of treatment is relative to a medicallyresponsive individual.

Various embodiments of the present invention provide for the treatmentof subjects diagnosed with MR-UC. MR-UC subjects are refractory tocurrent conventional medical therapy used, such as anti-TNF therapy,thiopurine therapy, corticosteroids and cyclosporine. In variousembodiments, the subjects diagnosed with MR-UC are treated withnon-conventional treatments, such as, but not limited to treatments thatmimics, modulates and/or targets RNASET2, TL1A and/or IFN-γ. In variousembodiments, treatments that mimics, modulates and/or targets RNASET2,TL1A and/or IFN-γ can comprise antibodies and or silencingoligonucleotides. In various embodiments, the subject diagnosed withMR-UC is determined to need RNASET2 mediated therapy, such as but notlimited to recombinant RNASET2 and anti-ICAM1. In various embodiments,the RNASET2 mediated therapy is an antibody or small molecule thattargets genes that are upstream and/or downstream of RNASET2.

In other embodiments, the process for subject identification and/orstratification described herein comprises determining the presence ofone or more risk variants. In certain embodiments, the one or more riskvariants comprise rs1819333, rs2149092, rs9355610, rs2149085, rs1410295or rs9366093. In various embodiments, the process comprises identifyingthe subject with IBD in need of treatment if 2, 3, 4, 5 or 6 RNASET2risk variants as described herein are present. In various embodiments,the risk allele for rs2149085 is the T allele. In various otherembodiments, the RNASET2 risk variants are the RNASET2 risk variantrs429083 and an RNASET2 risk variant selected from the group consistingof rs1819333, rs2149092, rs9355610, rs2149085, rs1410295, rs9366093, andcombinations thereof. In various other embodiments, the RNASET2 riskvariants is one or more of the RNASET2 risk variants in Tables 2, 3, 4,5, 6, 7, 8, 9, 10, and 13 and an RNASET2 risk variant selected from thegroup consisting of rs1819333, rs2149092, rs9355610, rs2149085,rs1410295, rs9366093, and combinations thereof. In various otherembodiments, the one or more risk variants at the RNASET2 gene isrs1819333, rs2149092, rs9355610 or rs2149085. In various embodiments,the subject is diagnosed with IBD if 2, 3, or 4, RNASET2 risk variantsrs1819333, rs2149092, rs9355610 or rs2149085 as described herein arepresent. In various other embodiments, the detection of the riskvariants in the biological sample stratifies the subject into a groupneeding treatment. In other embodiments, the presence of a greaternumber of risk variants in the sample indicates that the subject is ingreater need of treatment. In some embodiments, the detection of RNASET2risk variants is indicative of the need for treatment in the subject. Insome embodiments, the subject is identified as needing anti-TL1Atherapy. In various embodiments, the subject identified as needingRNASET2 mediated therapy, such as but not limited to recombinant RNASET2and anti-ICAM1. In various embodiments, the RNASET2 mediated therapy isan antibody or small molecule that targets genes that are upstreamand/or downstream of RNASET2.

In various embodiments, the detection of RNASET2 risk variants can beaccomplished by analyzing nucleic acids of a biological sample from thesubject, as discussed herein.

In other embodiments, the process for subject identification and/orstratification described herein further comprises assaying the sample todetect the level of RNASET2 methylation, relative to a healthyindividual. In some embodiments, a subject with an increased level ofRNASET2 methylation is identified as a subject in need of treatment. Insome embodiments, the sample is assessed for the level of RNASET2methylation and one or more RNASET2 risk variants. In certainembodiments, a subject who has an increase in RNASET2 methylation andthe presence of one or more RNASET2 risk variants is identified as asubject in need of treatment. In other embodiments, the sample isassessed for the level of RNASET2 methylation and the expression levelsof RNASET2, TL1A and/or IFN-γ. In certain embodiments, a subject who hasan increase in RNASET2 methylation and a decrease in RNASET2, anincrease in TL1A and/or IFN-γ is identified as a subject in need oftreatment. In certain embodiments, the subject is identified as needinga treatment that mimics, modulates and/or targets RNASET2, TL1A and/orIFN-γ. In various embodiments, treatments that mimics, modulates and/ortargets RNASET2, TL1A and/or IFN-γ can comprise antibodies and orsilencing oligonucleotides. In some embodiments, the subject isidentified as needing anti-TL1A therapy. In some embodiments, thesubject is identified as needing a treatment that causes a decrease inRNASET2 methylation. In various other embodiments, the detection of anincrease in RNASET2 methylation is indicative of a patient with severeCD requiring surgery. In a further embodiment, the subject is identifiedas needing a treatment that comprises colectomy and/or anti-TL1Atherapy.

In various other embodiments, the process for subject identificationand/or stratification described herein can further comprise assaying thesample to detect an increase or decrease of at least one microbialantigen (serological factor), relative to a healthy individual. In someembodiments, the microbial antigens (serological factors) assessedcomprise ANCA, ASCA, OmpC, 12 and CBir. In some embodiments, the sampleis assessed for one or more microbial antigens (serological factors) andone or more RNASET2 risk variants. In certain embodiments, a subject whohas one or more risk serological factors and the presence of one or moreRNASET2 risk variants is identified as a subject in need of treatment.In yet other embodiments, the sample is assessed for one or more riskserological factors and the expression levels of RNASET2, TL1A and/orIFN-γ. In certain embodiments, a subject who has one or more riskserological factors and a decrease in RNASET2, an increase in TL1Aand/or IFN-γ is identified as a subject in need of treatment. In someembodiments, the subject is identified as needing a treatment thatmimics, modulates and/or targets RNASET2, TL and/or IFNγ. In variousembodiments, treatments that mimics, modulates and/or targets RNASET2,TL1A and/or IFN-γ can comprise antibodies and or silencingoligonucleotides. In other embodiments, the treatment is anti-TL1Atherapy. In various embodiments, the treatment is an RNASET2 mediatedtherapy, such as but not limited to recombinant RNASET2 and anti-ICAM1.In various embodiments, the RNASET2 mediated therapy is an antibody orsmall molecule that targets genes that are upstream and/or downstream ofRNASET2.

In various embodiments the subject identified with IBD demonstratestherapeutic failure of thiopurine and anti-TNF therapy. In various otherembodiments, the subject identified with IBD is determined to needsurgical intervention. In some other embodiments, the surgicalintervention is intestinal resection. Various embodiments of the presentinvention also provide for a method of selecting surgery for a subjecthaving Inflammatory Bowel Disease, comprising: obtaining a sample fromthe subject; subjecting the sample to an assay adapted to determine thepresence or absence of one or more risk variants at the RNASET2 gene;diagnosing MR-UC in the subject based on the presence of one or morerisk variants at the RNASET2 gene; and selecting surgery for the subjectdiagnosed with MR-UC. In some embodiments, the one or more risk variantsat the RNASET2 gene is rs1819333, rs2149092, rs9355610, rs2149085,rs1410295 or rs9366093. In various other embodiments, the RNASET2 riskvariants are the RNASET2 risk variant rs429083 and an RNASET2 riskvariant selected from the group consisting of rs1819333, rs2149092,rs9355610, rs2149085, rs1410295, rs9366093, and combinations thereof. Invarious other embodiments, the RNASET2 risk variants is one or more ofthe RNASET2 risk variants in Tables 2, 3, 4, 5, 6, 7, 8, 9, 10, and 13and an RNASET2 risk variant selected from the group consisting ofrs1819333, rs2149092, rs9355610, rs2149085, rs1410295, rs9366093, andcombinations thereof. In various other embodiments, the one or more riskvariants at the RNASET2 gene is rs1819333, rs2149092, rs9355610 orrs2149085. In various embodiments, the subject is diagnosed with IBD if2, 3, or 4, RNASET2 risk variants rs1819333, rs2149092, rs9355610 orrs2149085 as described herein are present. In some embodiments, themethod further comprises determining the level of methylation ofRNASET2. In various embodiments, a subject with an increased level ofRNASET2 methylation is identified as a subject in need of surgery. Inother embodiments, the subject with an increase in RNASET2 methylationand the presence of one or more risk variants at the RNASET2 gene isidentified as a subject in need of surgery.

In various embodiments, the presence of one or more risk variants at theRNASET2 gene is associated with decreased expression of RNASET2. Inother embodiments, the presence of one or more risk variants at theRNASET2 gene is associated with decreased expression of RNASET2 inperipheral and mucosal tissues. In some other embodiments, the presenceof one or more risk variants at the RNASET2 gene is associated with DNAhypermethylation in patients requiring surgical intervention for diseasemanagement. In yet other embodiments, the presence of one or more riskvariants at the RNASET2 gene is associated with therapeutic failure ofthiopurine and/or anti-TNF therapy. In some other embodiments, thepresence of one or more risk variants at the RNASET2 gene is associatedwith ANCA sero-positivity. In various other embodiments, the presence ofone or more risk variants at the RNASET2 gene is associated withincreased overall length of intestinal resection.

Various embodiments of the present invention provide for a method ofselecting a therapy for a subject having Inflammatory Bowel Disease,comprising: obtaining a sample from the subject; subjecting the sampleto an assay adapted to determine the presence or absence of one or morerisk variants at the RNASET2 gene; diagnosing medically refractiveulcerative colitis (MR-UC) in the subject based on the presence of oneor more risk variants at the RNASET2 gene; and selecting surgery as thetherapy and not selecting thiopurine or anti-TNF as the therapy for thesubject diagnosed with MR-UC. In various embodiments, the one or morerisk variants at the RNASET2 gene is rs1819333, rs2149092, rs9355610,rs2149085, rs1410295 or rs9366093. In various other embodiments, theRNASET2 risk variants are the RNASET2 risk variant rs429083 and anRNASET2 risk variant selected from the group consisting of rs1819333,rs2149092, rs9355610, rs2149085, rs1410295, rs9366093, and combinationsthereof. In various other embodiments, the RNASET2 risk variants is oneor more of the RNASET2 risk variants in Tables 2, 3, 4, 5, 6, 7, 8, 9,10, and 13 and an RNASET2 risk variant selected from the groupconsisting of rs1819333, rs2149092, rs9355610, rs2149085, rs1410295,rs9366093, and combinations thereof. In various other embodiments, theone or more risk variants at the RNASET2 gene is rs1819333, rs2149092,rs9355610 or rs2149085. In various embodiments, the subject is diagnosedwith IBD if 2, 3, or 4, RNASET2 risk variants rs1819333, rs2149092,rs9355610 or rs2149085 as described herein are present. In yet otherembodiments, the method further comprises determining the level ofmethylation of RNASET2, wherein increased methylation is indicative of asubject requiring surgical intervention.

Various embodiments of the present invention provide for the treatmentof subjects diagnosed with MR-UC. MR-UC subjects are refractory tocurrent conventional medical therapy used, such as anti-TNF therapy,thiopurine therapy, corticosteroids and cyclosporine. In variousembodiments, the subjects diagnosed with MR-UC are treated withnon-conventional treatments, such as, but not limited to treatments thatmimics, modulates and/or targets RNASET2, TL1A and/or IFN-γ. In variousembodiments, treatments that mimics, modulates and/or targets RNASET2,TL1A and/or IFN-γ can comprise antibodies and or silencingoligonucleotides. In various embodiments, the subject diagnosed withMR-UC is determined to need RNASET2 mediated therapy, such as but notlimited to recombinant RNASET2 and anti-ICAM1. In various embodiments,the RNASET2 mediated therapy is an antibody or small molecule thattargets genes that are upstream and/or downstream of RNASET2.

Detection of Methylation

Various embodiments provide for a method of diagnosing a subject withinflammatory bowel disease (IBD). In some embodiments, the methodcomprises determining the level of methylation of RNASET2; andidentifying the subject with IBD as a subject with increased RNASET2methylation. In other embodiments, the method comprises identifying thesubject with IBD as a subject who has increased RNASET2 methylation andwho has the presence of one or more risk variants at the RNASET2 gene.In various other embodiments, the method comprises determining theexpression level of RNASET2, TL1A and/or IFN-γ; and diagnosing thesubject with IBD if the subject has a decrease in RNASET2, an increasein TL1A, an increase in IFN-γ and/or an increase in RNASET2 methylation.

Various embodiments provide for a process of identifying a subject withinflammatory bowel disease (IBD) in need of treatment. In someembodiments, the method comprises determining the level of methylationof RNASET2; and identifying the subject in need of treatment as asubject with increased RNASET2 methylation. In other embodiments, theexpression level of RNASET2, TL1A and/or IFN-γ and the level ofmethylation of RNASET2 are determined, to identify a subject withinflammatory bowel disease in need of treatment. In various embodiments,the method comprises determining a subject in need of treatment as asubject who has a decrease in RNASET2, an increase in TL1A, an increasein IFN-γ, and/or an increase in RNASET2 methylation. In various otherembodiments, the method comprises determining the presence or absence ofone or more risk variants at the RNASET2 gene and identifying a subjectwith IBD in need of treatment as a subject who has an increase inRNASET2 methylation and the presence of one or more RNASET2 riskvariants.

In various embodiments, an increase in methylation is indicative of asubject requiring surgical intervention. In yet other embodiments, anincrease in RNASET2 methylation is indicative of requiring surgicalintervention.

Various methods to detect levels of methylation include, but are notlimited to the following assays, mass spectrometry, methylation-specificPCR (MSP), whole genome bisulfite sequencing, (BS-Seq), the HELP assay,ChIP-on-chip assays, restriction landmark genomic scanning, methylatedDNA immunoprecipitation (MeDIP, MeDIP-chip, MeDIPseq), pyrosequencing ofbisulfite treated DNA, molecular break light assay for DNA adeninemethyltransferase activity, methyl sensitive southern blotting, separatenative DNA into methylated and unmethylated fractions using MethylCpGBinding Proteins (MBPs) and/or Methyl Binding Domain (MBD),MethylationEPIC BeadChip, Illumina Infinium Methylation 450 BeadChip,High Resolution Melt Analysis (FIRM or HRMA), and/or ancient DNAmethylation reconstruction.

Various embodiments of the invention provide for the treatment of asubject diagnosed with inflammatory bowel disease (IBD) by the methodcomprising obtaining a sample from the subject; subjecting the sample toan assay adapted to determine the presence or absence of one or morerisk variants at the RNASET2 gene; and diagnosing IBD in the subjectbased on the presence of one or more risk variants at the RNASET2 gene.In various embodiments, inflammatory bowel disease is Crohn's disease,ulcerative colitis or medically refractive ulcerative colitis.

Various embodiments of the invention provide for the treatment of asubject diagnosed with medically refractive ulcerative colitis (MR-UC)by the method comprising, obtaining a sample from the subject;subjecting the sample to an assay adapted to determine the presence orabsence of one or more risk variants at the RNASET2; and diagnosingMR-UC in the subject based on the presence of one or more risk variantsat the RNASET2 gene.

Various embodiments of the present invention provide for the treatmentof subjects diagnosed with MR-UC. MR-UC subjects are refractory tocurrent conventional medical therapy used, such as anti-TNF therapy andthiopurine therapy. In various embodiments, the subjects diagnosed withMR-UC are treated with non-conventional treatments, such as, but notlimited to treatments that mimics, modulates and/or targets RNASET2,TL1A and/or IFN-γ. In various embodiments, treatments that mimics,modulates and/or targets RNASET2, TL1A and/or IFN-γ can compriseantibodies and or silencing oligonucleotides. In various embodiments,the subject diagnosed with MR-UC is determined to need RNASET2 mediatedtherapy, such as but not limited to recombinant RNASET2 and anti-ICAM1.In various embodiments, the RNASET2 mediated therapy is an antibody orsmall molecule that targets genes that are upstream and/or downstream ofRNASET2.

Biological Samples, Sample Preparation and Gene Expression Detection

In various embodiments, the steps involved in the current inventioncomprise obtaining a biological sample from a subject. The biologicalsample may be obtained either through surgical biopsy or surgicalresection. Alternatively, a sample can be obtained through primarypatient derived cell lines, or archived patient samples in the form ofFFPE (Formalin fixed, paraffin embedded) samples, or fresh frozensamples. A sample may also comprise whole blood, peripheral blood,plasma, serum, saliva, cheek swab, or other bodily fluid or tissue. Invarious embodiments, the sample comprises tissue from the large and/orsmall intestine. In various other embodiments, the large intestinesample comprises the cecum, colon (the ascending colon, the transversecolon, the descending colon, and the sigmoid colon), rectum and/or theanal canal. In yet other embodiments, the small intestine samplecomprises the duodenum, jejunum, and/or the ileum.

Nucleic acid or protein samples derived from the biological sample(i.e., tissue and/or cells) of a subject that can be used in the methodsof the invention can be prepared by means well known in the art. Forexample, surgical procedures or needle biopsy aspiration can be used tocollect the biological samples from a subject. In some embodiments, itis important to enrich and/or purify the abnormal tissue and/or cellsamples from the normal tissue and/or cell samples. In otherembodiments, the abnormal tissue and/or cell samples can then bemicrodissected to reduce the amount of normal tissue contamination priorto extraction of genomic nucleic acid or pre-RNA for use in the methodsof the invention. Such enrichment and/or purification can beaccomplished according to methods well-known in the art, such as needlemicrodissection, laser microdissection, fluorescence activated cellsorting, and immunological cell sorting.

Analysis of the nucleic acid and/or protein from an individual may beperformed using any of various techniques. In various embodiments,assaying gene expression levels for RNASET2 comprises northern blot,reverse transcription PCR, real-time PCR, serial analysis of geneexpression (SAGE), DNA microarray, tiling array, RNA-Seq, or acombination thereof. In various other embodiments, the gene expressionlevels for RNASET2, TL1A and/or IFN-γ are assayed. In other embodiments,the level of RNASET2 methylation is determined.

In various embodiments, methods and systems to detect protein expressioninclude but are not limited to ELISA, immunohistochemistry, westernblot, flow cytometry, fluorescence in situ hybridization (FISH),radioimmuno assays, and affinity purification.

The analysis of gene expression levels may involve amplification of anindividual's nucleic acid by the polymerase chain reaction. Use of thepolymerase chain reaction for the amplification of nucleic acids is wellknown in the art (see, for example, Mullis et al. (Eds.), The PolymeraseChain Reaction, Birkhauser, Boston, (1994)).

Methods of “quantitative” amplification are well known to those of skillin the art. For example, quantitative PCR involves simultaneouslyco-amplifying a known quantity of a control sequence using the sameprimers. This provides an internal standard that may be used tocalibrate the PCR reaction. Detailed protocols for quantitative PCR areprovided in Innis, et al. (1990) PCR Protocols, A Guide to Methods andApplications, Academic Press, Inc. N.Y.). Measurement of DNA copy numberat microsatellite loci using quantitative PCR analysis is described inGinzonger, et al. (2000) Cancer Research 60:5405-5409. The known nucleicacid sequence for the genes is sufficient to enable one of skill in theart to routinely select primers to amplify any portion of the gene.Fluorogenic quantitative PCR may also be used in the methods of theinvention. In fluorogenic quantitative PCR, quantitation is based onamount of fluorescence signals, e.g., TaqMan and sybr green.

Other suitable amplification methods include, but are not limited to,ligase chain reaction (LCR) (see Wu and Wallace (1989) Genomics 4: 560,Landegren, et al. (1988) Science 241:1077, and Barringer et al. (1990)Gene 89: 117), transcription amplification (Kwoh, et al. (1989) Proc.Natl. Acad. Sci. USA 86: 1173), self-sustained sequence replication(Guatelli, et al. (1990) Proc. Nat. Acad. Sci. USA 87: 1874), dot PCR,and linker adapter PCR, etc.

A DNA sample suitable for hybridization can be obtained, e.g., bypolymerase chain reaction (PCR) amplification of genomic DNA, fragmentsof genomic DNA, fragments of genomic DNA ligated to adaptor sequences orcloned sequences. Computer programs that are well known in the art canbe used in the design of primers with the desired specificity andoptimal amplification properties, such as Oligo version 5.0 (NationalBiosciences). PCR methods are well known in the art, and are described,for example, in Innis et al., eds., 1990, PCR Protocols: A Guide toMethods And Applications, Academic Press Inc., San Diego, Calif. It willbe apparent to one skilled in the art that controlled robotic systemsare useful for isolating and amplifying nucleic acids and can be used.

Hybridization

The nucleic acid samples derived from a subject used in the methods ofthe invention can be hybridized to arrays comprising probes (e.g.,oligonucleotide probes) in order to identify RNASET2, TL1A and/or IFN-γand in instances wherein a housekeeping gene expression is also to beassessed, comprising probes in order to identify selected housekeepinggenes. In particular embodiments, the probes used in the methods of theinvention comprise an array of probes that can be tiled on a DNA chip(e.g., SNP oligonucleotide probes). Hybridization and wash conditionsused in the methods of the invention are chosen so that the nucleic acidsamples to be analyzed by the invention specifically bind orspecifically hybridize to the complementary oligonucleotide sequences ofthe array, preferably to a specific array site, wherein itscomplementary DNA is located. In some embodiments, the complementary DNAcan be completely matched or mismatched to some degree as used, forexample, in Affymetrix oligonucleotide arrays. The single-strandedsynthetic oligodeoxyribonucleic acid DNA probes of an array may need tobe denatured prior to contact with the nucleic acid samples from asubject, e.g., to remove hairpins or dimers which form due toself-complementary sequences.

Optimal hybridization conditions will depend on the length of the probesand type of nucleic acid samples from a subject. General parameters forspecific (i.e., stringent) hybridization conditions for nucleic acidsare described in Sambrook and Russel, Molecular Cloning: A LaboratoryManual 4^(th) ed., Cold Spring Harbor Laboratory Press (Cold SpringHarbor, N.Y. 2012); Ausubel et al., eds., 1989, Current Protocols inMolecules Biology, Vol. 1, Green Publishing Associates, Inc., John Wiley& Sons, Inc., New York, at pp. 2.10.1-2.10.16. Exemplary usefulhybridization conditions are provided in, e.g., Tijessen, 1993,Hybridization with Nucleic Acid Probes, Elsevier Science Publishers B.V. and Kricka, 1992, Nonisotopic DNA Probe Techniques, Academic Press,San Diego, Calif.

Oligonucleotide Nucleic Acid Arrays

In some embodiments of the methods of the present invention, DNA arrayscan be used to determine the expression levels of genes, by measuringthe level of hybridization of the nucleic acid sequence tooligonucleotide probes that comprise complementary sequences. Variousformats of DNA arrays that employ oligonucleotide “probes,” (i.e.,nucleic acid molecules having defined sequences) are well known to thoseof skill in the art. Typically, a set of nucleic acid probes, each ofwhich has a defined sequence, is immobilized on a solid support in sucha manner that each different probe is immobilized to a predeterminedregion. In certain embodiments, the set of probes forms an array ofpositionally-addressable binding (e.g., hybridization) sites on asupport. Each of such binding sites comprises a plurality ofoligonucleotide molecules of a probe bound to the predetermined regionon the support. More specifically, each probe of the array is preferablylocated at a known, predetermined position on the solid support suchthat the identity (i.e., the sequence) of each probe can be determinedfrom its position on the array (i.e., on the support or surface).Microarrays can be made in a number of ways, of which several aredescribed herein. However produced, microarrays share certaincharacteristics, they are reproducible, allowing multiple copies of agiven array to be produced and easily compared with each other.

In some embodiments, the microarrays are made from materials that arestable under binding (e.g., nucleic acid hybridization) conditions. Themicroarrays are preferably small, e.g., between about 1 cm² and 25 cm²,preferably about 1 to 3 cm². However, both larger and smaller arrays arealso contemplated and may be preferable, e.g., for simultaneouslyevaluating a very large number of different probes. Oligonucleotideprobes can be synthesized directly on a support to form the array. Theprobes can be attached to a solid support or surface, which may be made,e.g., from glass, plastic (e.g., polypropylene, nylon), polyacrylamide,nitrocellulose, gel, or other porous or nonporous material. The set ofimmobilized probes or the array of immobilized probes is contacted witha sample containing labeled nucleic acid species so that nucleic acidshaving sequences complementary to an immobilized probe hybridize or bindto the probe. After separation of, e.g., by washing off, any unboundmaterial, the bound, labeled sequences are detected and measured. Themeasurement is typically conducted with computer assistance. DNA arraytechnologies have made it possible to determine the expression level ofRNASET2, TL1A and/or IFN-γ, housekeeping genes and the methylation stateof RNASET2.

In certain embodiments, high-density oligonucleotide arrays are used inthe methods of the invention. These arrays containing thousands ofoligonucleotides complementary to defined sequences, at definedlocations on a surface can be synthesized in situ on the surface by, forexample, photolithographic techniques (see, e.g., Fodor et al., 1991,Science 251:767-773; Pease et al., 1994, Proc. Natl. Acad. Sci. U.S.A.91:5022-5026; Lockhart et al., 1996, Nature Biotechnology 14:1675; U.S.Pat. Nos. 5,578,832; 5,556,752; 5,510,270; 5,445,934; 5,744,305; and6,040,138). Methods for generating arrays using inkjet technology for insitu oligonucleotide synthesis are also known in the art (see, e.g.,Blanchard, International Patent Publication WO 98/41531, published Sep.24, 1998; Blanchard et al., 1996, Biosensors And Bioelectronics11:687-690; Blanchard, 1998, in Synthetic DNA Arrays in GeneticEngineering, Vol. 20, J. K. Setlow, Ed., Plenum Press, New York at pages111-123). Another method for attaching the nucleic acids to a surface isby printing on glass plates, as is described generally by Schena et al.(1995, Science 270:467-470). Other methods for making microarrays, e.g.,by masking (Maskos and Southern, 1992, Nucl. Acids. Res. 20:1679-1684),may also be used. When these methods are used, oligonucleotides (e.g.,15 to 60-mers) of known sequence are synthesized directly on a surfacesuch as a derivatized glass slide. The array produced can be redundant,with several oligonucleotide molecules corresponding to each informativelocus of interest (e.g., SNPs, RFLPs, STRs, etc.).

One exemplary means for generating the oligonucleotide probes of the DNAarray is by synthesis of synthetic polynucleotides or oligonucleotides,e.g., using N-phosphonate or phosphoramidite chemistries (Froehler etal., 1986, Nucleic Acid Res. 14:5399-5407; McBride et al., 1983,Tetrahedron Lett. 24:246-248). Synthetic sequences are typically betweenabout 15 and about 600 bases in length, more typically between about 20and about 100 bases, most preferably between about 40 and about 70 basesin length. In some embodiments, synthetic nucleic acids includenon-natural bases, such as, but by no means limited to, inosine. Asnoted above, nucleic acid analogues may be used as binding sites forhybridization. An example of a suitable nucleic acid analogue is peptidenucleic acid (see, e.g., Egholm et al., 1993, Nature 363:566-568; U.S.Pat. No. 5,539,083). In alternative embodiments, the hybridization sites(i.e., the probes) are made from plasmid or phage clones of regions ofgenomic DNA corresponding to SNPs or the complement thereof. The size ofthe oligonucleotide probes used in the methods of the invention can beat least 10, 20, 25, 30, 35, 40, 45, or 50 nucleotides in length. It iswell known in the art that although hybridization is selective forcomplementary sequences, other sequences which are not perfectlycomplementary may also hybridize to a given probe at some level. Thus,multiple oligonucleotide probes with slight variations can be used, tooptimize hybridization of samples. To further optimize hybridization,hybridization stringency condition, e.g., the hybridization temperatureand the salt concentrations, may be altered by methods that are wellknown in the art.

In various embodiments, the high-density oligonucleotide arrays used inthe methods of the invention comprise oligonucleotides corresponding toRNASET2, TL1A and/or IFN-γ and housekeeping genes. In other embodiments,the oligonucleotides correspond to methylated RNASET2. Theoligonucleotide probes may comprise DNA or DNA “mimics” (e.g.,derivatives and analogues) corresponding to a portion of eachinformative locus of interest (e.g., SNPs, RFLPs, STRs, etc.) in asubject's genome. The oligonucleotide probes can be modified at the basemoiety, at the sugar moiety, or at the phosphate backbone. Exemplary DNAmimics include, e.g., phosphorothioates. For each SNP locus, a pluralityof different oligonucleotides may be used that are complementary to thesequences of sample nucleic acids. For example, for a single informativelocus of interest (e.g., SNPs, RFLPs, STRs, etc.) about 2, 3, 4, 5, 6,7, 8, 9, 10, 11, 12, 13, 14, 15, 16, 17, 18, 19, 20, 21, 22, 23, 24, 25,26, 27, 28, 29, 30, 31, 32, 33, 34, 35, 36, 37, 38, 39, 40, 41, 42, 43,44, 45, 46, 47, 48, 49, 50, or more different oligonucleotides can beused. Each of the oligonucleotides for a particular informative locus ofinterest may have a slight variation in perfect matches, mismatches, andflanking sequence around the SNP. In certain embodiments, the probes aregenerated such that the probes for a particular informative locus ofinterest comprise overlapping and/or successive overlapping sequenceswhich span or are tiled across a genomic region containing the targetsite, where all the probes contain the target site. By way of example,overlapping probe sequences can be tiled at steps of a predeterminedbase interval, e. g. at steps of 1, 2, 3, 4, 5, 6, 7, 8, 9, or 10 basesintervals. In certain embodiments, the assays can be performed usingarrays suitable for use with molecular inversion probe protocols such asdescribed by Wang et al. (2007) Genome Biol. 8, R246. Foroligonucleotide probes targeted at nucleic acid species of closelyresembled (i.e., homologous) sequences, “cross-hybridization” amongsimilar probes can significantly contaminate and confuse the results ofhybridization measurements. Cross-hybridization is a particularlysignificant concern in the detection of SNPs since the sequence to bedetected (i.e., the particular SNP) must be distinguished from othersequences that differ by only a single nucleotide. Cross-hybridizationcan be minimized by regulating either the hybridization stringencycondition and/or during post-hybridization washings. Highly stringentconditions allow detection of allelic variants of a nucleotide sequence,e.g., about 1 mismatch per 10-30 nucleotides. There is no singlehybridization or washing condition which is optimal for all differentnucleic acid sequences, these conditions can be identical to thosesuggested by the manufacturer or can be adjusted by one of skill in theart. In some embodiments, the probes used in the methods of theinvention are immobilized (i.e., tiled) on a glass slide called a chip.For example, a DNA microarray can comprises a chip on whicholigonucleotides (purified single-stranded DNA sequences in solution)have been robotically printed in an (approximately) rectangular arraywith each spot on the array corresponds to a single DNA sample whichencodes an oligonucleotide. In summary the process comprises, floodingthe DNA microarray chip with a labeled sample under conditions suitablefor hybridization to occur between the slide sequences and the labeledsample, then the array is washed and dried, and the array is scannedwith a laser microscope to detect hybridization. In certain embodimentsthere are at least 250, 500, 1,000, 2,000, 3,000, 4,000, 5,000, 6,000,7,000, 8,000, 9,000, 10,000, 11,000, 12,000, 13,000, 14,000, 15,000,16,000, 17,000, 18,000, 19,000, 20,000, 21,000, 22,000, 23,000, 24,000,25,000, 26,000, 27,000, 28,000, 29,000, 30,000, 31,000, 32,000, 33,000,34,000, 35,000, 36,000, 37,000, 38,000, 39,000, 40,000, 41,000, 42,000,43,000, 44,000, 45,000, 50,000, 60,000, 70,000, 80,000, 90,000, 100,000or more or any range in between, of RNASET2, TL1A and/or IFN-γ orhousekeeping genes for which probes appear on the array (withmatch/mismatch probes for a single locus of interest or probes tiledacross a single locus of interest counting as one locus of interest).The maximum number of RNASET2, TL1A and/or IFN-γ or housekeeping genesbeing probed per array is determined by the size of the genome andgenetic diversity of the subjects species. DNA chips are well known inthe art and can be purchased in pre-5 fabricated form with sequencesspecific to particular species. In other embodiments, SNPs and/or DNAcopy number can be detected and quantitated using sequencing methods,such as “next-generation sequencing methods” as described further above.

Labeling

In some embodiments, the protein, polypeptide, nucleic acid, fragmentsthereof, or fragments thereof ligated to adaptor regions used in themethods of the invention are detectably labeled. For example, thedetectable label can be a fluorescent label, e.g., by incorporation ofnucleotide analogues. Other labels suitable for use in the presentinvention include, but are not limited to, biotin, iminobiotin,antigens, cofactors, dinitrophenol, lipoic acid, olefinic compounds,detectable polypeptides, electron rich molecules, enzymes capable ofgenerating a detectable signal by action upon a substrate, andradioactive isotopes.

Radioactive isotopes include that can be used in conjunction with themethods of the invention, but are not limited to, 32P and 14C.Fluorescent molecules suitable for the present invention include, butare not limited to, fluorescein and its derivatives, rhodamine and itsderivatives, texas red, 5′carboxy-fluorescein (“FAM”), 2′,7′-dimethoxy-4′, 5′-dichloro-6-carboxy-fluorescein (“JOE”), N, N, N′,N′-tetramethyl-6-carboxy-rhodamine (“TAMRA”), 6-carboxy-X-rhodamine(“ROX”), HEX, TET, IRD40, and IRD41.

Fluorescent molecules which are suitable for use according to theinvention further include: cyamine dyes, including but not limited toCy2, Cy3, Cy3.5, CY5, Cy5.5, Cy7 and FLUORX; BODIPY dyes including butnot limited to BODIPY-FL, BODIPY-TR, BODIPY-TMR, BODIPY-630/650, andBODIPY-650/670; and ALEXA dyes, including but not limited to ALEXA-488,ALEXA-532, ALEXA-546, ALEXA-568, and ALEXA-594; as well as otherfluorescent dyes which will be known to those who are skilled in theart. Electron rich indicator molecules suitable for the presentinvention include, but are not limited to, ferritin, hemocyanin andcolloidal gold.

Two-color fluorescence labeling and detection schemes may also be used(Shena et al., 1995, Science 270:467-470). Use of two or more labels canbe useful in detecting variations due to minor differences inexperimental conditions (e.g., hybridization conditions). In someembodiments of the invention, at least 5, 10, 20, or 100 dyes ofdifferent colors can be used for labeling. Such labeling would alsopermit analysis of multiple samples simultaneously which is encompassedby the invention.

The labeled nucleic acid samples, fragments thereof, or fragmentsthereof ligated to adaptor regions that can be used in the methods ofthe invention are contacted to a plurality of oligonucleotide probesunder conditions that allow sample nucleic acids having sequencescomplementary to the probes to hybridize thereto. Depending on the typeof label used, the hybridization signals can be detected using methodswell known to those of skill in the art including, but not limited to,X-Ray film, phosphor imager, or CCD camera. When fluorescently labeledprobes are used, the fluorescence emissions at each site of a transcriptarray can be, preferably, detected by scanning confocal lasermicroscopy. In one embodiment, a separate scan, using the appropriateexcitation line, is carried out for each of the two fluorophores used.Alternatively, a laser can be used that allows simultaneous specimenillumination at wavelengths specific to the two fluorophores andemissions from the two fluorophores can be analyzed simultaneously (seeShalon et al. (1996) Genome Res. 6, 639-645). In a preferred embodiment,the arrays are scanned with a laser fluorescence scanner with a computercontrolled X-Y stage and a microscope objective. Sequential excitationof the two fluorophores is achieved with a multi-line, mixed gas laser,and the emitted light is split by wavelength and detected with twophotomultiplier tubes. Such fluorescence laser scanning devices aredescribed, e.g., in Schena et al. (1996) Genome Res. 6, 639-645.Alternatively, a fiber-optic bundle can be used such as that describedby Ferguson et al. (1996) Nat. Biotech. 14, 1681-1684. The resultingsignals can then be analyzed to determine the expression of RNASET2,TL1A and/or IFN-γ and housekeeping genes, using computer software.

In other embodiments, where genomic DNA of a subject is fragmented usingrestriction endonucleases and amplified prior to analysis, theamplification can comprise cloning regions of genomic DNA of thesubject. In such methods, amplification of the DNA regions is achievedthrough the cloning process. For example, expression vectors can beengineered to express large quantities of particular fragments ofgenomic DNA of the subject (Sambrook and Russel, Molecular Cloning: ALaboratory Manual 4^(th) ed., Cold Spring Harbor Laboratory Press (ColdSpring Harbor, N.Y. 2012)).

In yet other embodiments, where the DNA of a subject is fragmented usingrestriction endonucleases and amplified prior to analysis, theamplification comprises expressing a nucleic acid encoding a gene, or agene and flanking genomic regions of nucleic acids, from the subject.RNA (pre-messenger RNA) that comprises the entire transcript includingintrons is then isolated and used in the methods of the invention toanalyze and provide a genetic signature of a cancer. In certainembodiments, no amplification is required. In such embodiments, thegenomic DNA, or pre-RNA, of a subject may be fragmented usingrestriction endonucleases or other methods. The resulting fragments maybe hybridized to SNP probes. Typically, greater quantities of DNA areneeded to be isolated in comparison to the quantity of DNA or pre-mRNAneeded where fragments are amplified. For example, where the nucleicacid of a subject is not amplified, a DNA sample of a subject for use inhybridization may be about 400 ng, 500 ng, 600 ng, 700 ng, 800 ng, 900ng, or 1000 ng of DNA or greater. Alternatively, in other embodiments,methods are used that require very small amounts of nucleic acids foranalysis, such as less than 400 ng, 300 ng, 200 ng, 100 ng, 90 ng, 85ng, 80 ng, 75 ng, 70 ng, 65 ng, 60 ng, 55 ng, 50 ng, or less, such as isused for molecular inversion probe (MIP) assays. These techniques areparticularly useful for analyzing clinical samples, such as paraffinembedded formalin-fixed material or small core needle biopsies,characterized as being readily available but generally having reducedDNA quality (e.g., small, fragmented DNA) and/or not providing largeamounts of nucleic acids.

Once the expression levels have been determined, the resulting data canbe analyzed using various algorithms, based on well-known methods usedby those skilled in the art.

Kits

The present invention is also directed to a kit to diagnose a subjectwith IBD

and/or identifying a subject in need of treatment. The kit is useful forpracticing the inventive method of diagnosing a subject and/oridentifying a subject in need of treatment. The kit is an assemblage ofmaterials or components, including at least one of the inventivecompositions. Thus, in some embodiments the kit contains a compositionincluding primers and probes for RNASET2, TL1A and/or IFN-γ, asdescribed above.

The exact nature of the components configured in the inventive kitdepends on its intended purpose. For example, some embodiments areconfigured for the purpose of assessing risk variants and/or geneexpression levels. In some embodiments, the kit is configured to detectthe gene expression levels of RNASET2 in a sample. In yet otherembodiments, the kit is configured to detect the gene expression levelsof RNASET2 and/or TL1A in a sample. In some other embodiments, the kitis configured to detect the gene expression levels of RNASET2, TL1Aand/or IFN-γ in a sample. In various other embodiments, the kit isconfigured to detect RNASET2 risk variants in a sample. In yet otherembodiments, the kit is configured to detect the level of RNASET2methylation in a sample. In one embodiment, the kit is configuredparticularly for the purpose of assessing mammalian subjects. In anotherembodiment, the kit is configured particularly for the purpose ofassessing human subjects. In further embodiments, the kit is configuredfor veterinary applications, assessing subjects such as, but not limitedto, farm animals, domestic animals, and laboratory animals.

Instructions for use may be included in the kit. “Instructions for use”typically include a tangible expression describing the technique to beemployed in using the components of the kit to effect a desired outcome,such as to diagnose a subject with IBD and/or identify a subject withIBD in need of treatment. Optionally, the kit also contains other usefulcomponents, such as, primers, diluents, buffers, pipetting or measuringtools or other useful paraphernalia as will be readily recognized bythose of skill in the art.

The materials or components assembled in the kit can be provided to thepractitioner stored in any convenient and suitable ways that preservetheir operability and utility. For example the components can be indissolved, dehydrated, or lyophilized form; they can be provided atroom, refrigerated or frozen temperatures. The components are typicallycontained in suitable packaging material(s). As employed herein, thephrase “packaging material” refers to one or more physical structuresused to house the contents of the kit, such as inventive compositionsand the like. The packaging material is constructed by well-knownmethods, preferably to provide a sterile, contaminant-free environment.The packaging materials employed in the kit are those customarilyutilized in gene expression assays. As used herein, the term “package”refers to a suitable solid matrix or material such as glass, plastic,paper, foil, and the like, capable of holding the individual kitcomponents. Thus, for example, a package can be a glass vial used tocontain suitable quantities of an inventive composition containingprimers and probes for RNASET2, TL1A, IFN-γ and/or RNASET2 methylation.The packaging material generally has an external label which indicatesthe contents and/or purpose of the kit and/or its components.

EXAMPLES

The following examples are provided to better illustrate the claimedinvention and are not to be interpreted as limiting the scope of theinvention. To the extent that specific materials are mentioned, it ismerely for purposes of illustration and is not intended to limit theinvention. One skilled in the art may develop equivalent means orreactants without the exercise of inventive capacity and withoutdeparting from the scope of the invention.

Example 1

Loss of RNASET2 in zebrafish results in accumulation of undigested rRNAwithin lysosomes. The major allele of RNASET2 (i) is a risk for IBD, CD(rs9355610), B1 and both ANCA levels and pos/neg (rs1410925) and (ii)protective for B3 and both ASCA IgA and IgG levels and pos/neg(rs1410925) (Table 2). The major allele rs9355610 is associated withlower levels of RNASET2 mRNA expression in CD small intestine andrectum, EBV transformed B cells and CD3+ PBL from IBD patients. Themajor allele is also associated with RNASET2 mRNA in CD sigmoid colon.Low levels of RNASET2 and increased levels of pANCA are associated withthe major allele. Methylation at the RNASET2 locus is inverselycorrelated with RNASET2 mRNA expression.

TABLE 2 Non-Jewish Qualitative and Quantitative Trait Association DataA1- iCHip CH BP minor Test NMISS OR STAT *P rs9355610 CD 6 167383075 AADD 3859 0.754 −4.041 5.33E−05 minor IBD 6 167383075 A ADD 4172 0.8591−2.607 9.12E−03 allele protective Al- Trait CH BP minor Test NMISS STATP rs1410295 OR B1 6 167345503 C ADD 538 0.7168 −2.588 9.64E−03 minorANCA 6 167345503 C ADD 875 0.7365 −2.626 8.65E−03 allele protective B3 6167345503 C ADD 537 1.408 2.337 1.95E−02 minor ASCA 6 167345503 C ADD820 1.379 2.926 3.44E−03 allele IgG risk ASCA 6 167345503 C ADD 8201.216 1.843 6.53E−02 Panel BETA levels ANCA 6 167345503 C ADD 872 −4.608−3.137 1.77E−03 minor allele protective ASCA 6 167345503 C ADD 820 4.0242.363 1.84E−02 minor IgA allele ASCA 6 167345503 C ADD 820 5.745 2.8214.90E−03 risk IgG All Non-Jewish A1 A2 Non-Jewish CD A1 A2 CHR SNP MinorMajor MAF CHR SNP Minor Major MAF 6 rs1410295 C G 0.3541 6 rs1410295 C G0.3484 6 rs9355610 A G 0.3305 6 rs9355610 A G 0.2915 *Bonferroni p-value1.7E−04

TABLE 3 RNASET2 Major allele is a risk for IBD and CD in a non-Jewishcohort Pheno Pheno Pheno SNP CH A1 A2 NMISS OR P Type OR P type OR Ptype rs9355610 6 A G 5913 0.8218 4.50E−05 IBD 0.756 1.22E−06 CD 0.940.3695 UC rs1819333 6 C A 5813 0.8523 3.91E−04 IBD 0.782 4.04E−06 CD0.988 0.8575 UC * SNP CH A1 A2 MAF NCHROBS rs1819333 6 C A 0.4894 21278rs9355610 6 A G 0.3608 21278 A1 = minor allele; A2 = major allele

TABLE 4 Qualitative Trait Associations in non-Jewish CD. Major allele isrisk for colonic disease in non-Jewish CD. CD- A1 Phenotype CHR SNP BPA1 A2 NMISS OR STAT p Freq B1 6 rs62436418 167265792 G A 592 0.6992−2.853 4.33E−03 0.3787 B2 6 rs62436418 167265792 G A 592 1.395 −2.6488.09E−03 Colon 6 rs62436418 167265792 G A 593 0.6275 −3.161 1.57E−03 B26 rs9355610 167303065 A G 592 1.433 2.709 6.75E−03 0.3608 Colon 6rs9355610 167303065 A G 593 0.7299 −2.04 4.14E−02 A1 = minor allele; A2= major allele

TABLE 5 RNASET2 SNPs Associated with CD and IBD. Major allele is riskfor CD and IBD. Pheno type CHR SNP_rsid BP A1 A2 TEST NMISS OR STAT PLOCATION MAF CD 6 rs2149085 167291100 G A ADD 4360 0.8414 −4.0165.93E−05 INTERGENIC 0.4751 CD 6 rs1819333 167293537 C A ADD 4361 0.8446−3.93 8.51E−05 INTERGENIC 0.4753 CD 6 rs3823208 167267836 G A ADD 43610.8507 −3.64 2.73E−04 INTRON 0.3446 CD 6 rs62436418 167265762 G A ADD4361 0.8569 −3.539 4.01E−04 INTERGENIC 0.3861 CD 6 rs2769345 167286384 GA ADD 4361 0.8593 −3.53 4.15E−04 INTRON 0.4811 CD 6 rs9459813 167287827A T ADD 4361 0.8028 −3.104 1.91E−03 INTRON 0.1102 CD 6 rs2236313167280379 G A ADD 4361 0.8784 −3.016 2.56E−03 INTRON 0.4476 CD 6rs9355610 167303065 A G ADD 4361 0.9084 −2.163 3.05E−02 INTERGENIC0.3502 IBD 6 rs41269599 167267869 A G ADD 5110 0.844 −1.982 4.75E−02INTRON 0.0635 A1 = minor allele; A2 = major allele

TABLE 6 RNASET2 SNPs Associated with Subclinical Phenotypes of CD PHENOTYPE CHR RSID BP A1 A2 TEST NMISS OR STAT P LOCATION MAF PDM 6 rs3798303167274358 G A ADD 2093 1.38 3.019 2.54E−03 INTRON 0.09853 Iritis 6rs41269599 167267869 A G ADD 1436 2.806 2.973 2.95E−03 INTRON 0.06876Iritis 6 rs181130555 167277010 D — ADD 1434 2.744 2.932 3.37E−03 INTRON0.07108 Iritis 6 rs3777721 167272065 C G ADD 1436 2.761 2.92 3.50E−03INTRON 0.07084 Iritis 6 rs41269597 167267663 C G ADD 1436 2.711 2.8684.13E−03 INTRON 0.07234 Iritis 6 imm_6_167277028 167277028 A — ADD 14352.609 2.776 5.51E−03 INTRON 0.07369 Iritis 6 rs1079145 167280714 A G ADD1436 2.424 2.717 6.59E−03 INTRON 0.0893 Iritis 6 rs10946197 167268406 AC ADD 1436 0.3753 −2.717 6.60E−03 INTRON 0.256 PDM 6 rs3777723 167273691A G ADD 2093 1.334 2.648 8.09E−03 INTRON 0.09552 A1 = minor allele; A2 =major allele; D = deletion

TABLE 7 RNASET2 Associations with Subclinical Phenotypes in non-JewishCD Patients PHENO TYPE CHR RSID BP A1 A2 TEST NMISS OR STAT P MAF Iritis6 rs1079145 167280714 A G ADD 680 3.646 2.99 2.79E−03 0.07357 Iritis 6rs3777721 167272065 C G ADD 680 3.844 2.97 2.98E−03 0.05932 Iritis 6rs181130555 167277010 D — ADD 679 3.622 2.909 3.63E−03 0.0613 Iritis 6imm_6_167277028 167277028 A — ADD 679 3.511 2.848 4.40E−03 0.06168Iritis 6 rs3778439 167278341 A G ADD 680 3.535 2.671 7.55E−03 0.05277Iritis 6 rs3734246 167278058 A G ADD 680 3.535 2.671 7.55E−03 0.05277PDM 6 rs2769339 167275844 G A ADD 977 1.553 2.929 3.41E−03 0.09707 PDM 6rs2757045 167270953 G A ADD 977 1.499 2.73 6.34E−03 0.09977 PDM 6rs3798303 167274358 G A ADD 977 1.491 2.669 7.62E−03 0.09669 PDM 6rs2757048 167271110 A G ADD 977 1.479 2.637 8.37E−03 0.099 Uveitis 6rs3777723 167273691 A G ADD 674 3.78 2.657 7.89E−03 0.09091 A1 = minoralele; A2 = major allele; D = deletion

TABLE 8 RNASET2 Association with Serologies in CD Patients BETA/Phenotype CHR SNP_rsid BP A1 A2 TEST NMISS OR STAT P LOCATION MAF CBIR 6rs425145 167321292 G A ADD 2432 4.175 2.167 3.03E−02 INTERGENIC 0.1121CBIR 6 rs415356 167326817 G A ADD 2432 4.16 2.164 3.06E−02 INTERGENIC0.1121 CBIR 6 rs435359 167317604 G A ADD 2432 4.16 2.164 3.06E−02INTERGENIC 0.1123 CBIR 6 rs375883 167304704 T A ADD 2430 4.119 2.143.24E−02 INTERGENIC 0.112 CBIR 6 rs62438869 167320907 A G ADD 2432−3.722 −2.101 3.57E−02 INTERGENIC 0.1281 CBIR 6 rs9459813 167287827 A TADD 2432 4.073 2.015 4.40E−02 INTRON 0.09872 CBIR 6 rs443297 167304286 AG ADD 2432 3.978 1.972 4.88E−02 INTERGENIC 0.09947 IgG.ASCA 6 rs1410295167265493 C G ADD 2326 2.342 1.936 5.29E−02 INTERGENIC 0.3474 A1 = minorallele; A2 = major allele

TABLE 9 RNASET2 Associations with Serologies of non-Jewish CD PatientsSEROLOGY CHR RSID BP A1 A2 TEST NMISS BETA STAT P MAF ANCA 6 rs41269599167267869 A G ADD 1143 −7.159 −2.709 6.85E−03 0.05586 CBIR 6 rs9459813167287827 A T ADD 1208 8.021 2.854 4.40E−03 0.1159 CBIR 6 rs9459812167287711 A C ADD 1208 7.699 2.735 6.33E−03 0.1156 IgA.ASCA 6 rs3823208167267836 G A ADD 1130 4.153 3.102 1.97E−03 0.3139 IgG.ASCA 6 rs3823208167267836 G A ADD 1130 4.99 3.115 1.89E−03 0.3139 IgG.ASCA 6imm_6_167277028 167277028 A — ADD 1129 8.352 2.725 6.53E−03 0.06168 A1 =minor allele. A2 = major allele

TABLE 10 RNASET2 Associations with Expression in Small Bowel SNP_rsidgene beta p-value FDR rs72079749 RNASET2 0.151129328 1.66E−040.371075825 rs66591848 RNASET2 0.154066135 2.27E−04 0.42289639 rs1951459RNASET2 0.161888591 2.39E−04 0.429556929 rs4710149 RNASET2 0.1618885912.39E−04 0.429556929 rs933243 RNASET2 0.161888591 2.39E−04 0.429556929rs9355610 RNASET2 0.161888591 2.39E−04 0.429556929 rs9356551 RNASET20.161888591 2.39E−04 0.429556929 rs9366078 RNASET2 0.161888591 2.39E−040.429556929 rs1819333 RNASET2 0.15479148 3.22E−04 0.461149469 rs2013815RNASET2 0.15479148 3.22E−04 0.461149469 rs2149085 RNASET2 0.154791483.22E−04 0.461149469 rs2769345 RNASET2 0.128393311 3.08E−03 0.777560209rs2236313 RNASET2 0.096154247 3.09E−02 0.908151161 Major allele is riskfor small bowel expression.

TABLE 11 RNASET2 Associations for Expression in Large bowel snp_rsidgene beta t-stat p-value FDR CD Rectum rs683571 RNASET2 −0.57902−3.65206 0.00115 0.460077 Rectum rs2031846 RNASET2 −0.48099 −3.274690.002992 0.679028 Rectum rs62436763 RNASET2 −0.50894 −3.24339 0.0032350.692932 Rectum rs41463945 RNASET2 −0.58473 −3.11594 0.004434 0.693762Sigmoid rs162289 RNASET2 0.147287 2.955434 0.007311 0.619358 Sigmoidrs162291 RNASET2 0.147287 2.955434 0.007311 0.619358 Sigmoid rs162293RNASET2 0.147287 2.955434 0.007311 0.619358 Sigmoid rs162294 RNASET20.147287 2.955434 0.007311 0.619358 Sigmoid rs162295 RNASET2 0.1472872.955434 0.007311 0.619358 Sigmoid rs162297 RNASET2 0.147287 2.9554340.007311 0.619358 Sigmoid rs2236312 RNASET2 0.162431 3.419281 0.0024560.451404 Sigmoid rs3756838 RNASET2 0.14602 3.147931 0.00467 0.576607Sigmoid rs3798307 RNASET2 0.162431 3.419281 0.002456 0.451404 Sigmoidrs62436424 RNASET2 0.14602 3.147931 0.00467 0.576607 Sigmoid rs7772112RNASET2 0.14602 3.147931 0.00467 0.576607 Sigmoid rs9366076 RNASET20.14602 3.147931 0.00467 0.576607 UC Rectum rs57237533 RNASET2 0.5720023.665898 0.001643 0.436982 Rectum rs56213919 RNASET2 0.572002 3.6658980.001643 0.436982 Sigmoid rs10946198 RNASET2 −0.36397 −3.11588 0.0081920.704927 Sigmoid rs1819333 RNASET2 −0.36397 −3.11588 0.008192 0.704927Sigmoid rs2149085 RNASET2 −0.36397 −3.11588 0.008192 0.704927 Sigmoidrs2769345 RNASET2 −0.36397 −3.11588 0.008192 0.704927

TABLE 12 Hits with Small Bowel Tissue Expression Sub- Sm “Near Gene”Published IBD Phenotype Bowel Pathway EBV Pre-Clinical Genes in iCHIPAssociation eQTL eQTL Cellular Cell IBD Locus (pValue)* (CD)* pValuepValue Location Line Model RNASET IBD: B2, <1E-04 N/A Intra Yes No2_FGFR10P (9.7E−03) Serology RNASE cellular CD: T2 (RNSET 2) (5.3E−05)

TABLE 13 RNASET2 Exome CHIP Function Assoc dis SNP/rsID n.case n.ctrlCHR BP A1 A2 MAF NMISS OR P geneList GVS Locus CD exm- 5742 5725 61.7E+08 G A 0.4134 11467 0.8932 3.28E−05 RNASET2 intron IBD rs2236313IBD exm- 10523 5725 6 1.7E+08 G A 0.4145 16248 0.9219 0.00061 RNASET2intron IBD rs2236313 A1 = minor allele; A2 = major allele

Allele risk is defined by the Odds ratio (OR). When the A1 allele and anOR of <1 is depicted, then the major allele is the risk allele (A2 isrisk). If the OR is >1, then the minor allele (A1) is risk allele.Knowing A1 and the Odds Ratio allows you to determine which allele isrisk and which is protective.

Example 2

The molecular mechanisms of TL1A augmentation of inflammation viaenhanced IFN-γ expression were defined using RNAseq. CD4⁺ T cells wereanalyzed in untreated conditions or treated with IL12 and IL18 or IL12and IL18 and TLA1 at the 1 ug scale. On a 10 ng scale, CD4⁺ T cells wereanalyzed when treated with IL12 and IL18 and TLA1, either with orwithout IFN-γ. The RNAseq data prescreen removed all failed probe data,all genes with fewer than 3 samples with FPKM>5. Using this criteria,8695 genes passed the prescreen and BRB Array Tools were used for classcomparison using paired samples.

The inventors demonstrate that at the molecular level, TL1A treatmentmediates enhanced expression of IFN-γ, in addition to mediating adecreased expression of RNASET2. The decreased expression of RNASET2 isdetected in CD patients: 1) with chronically active disease, 2) withrefractive disease requiring surgical intervention, 3) with patientsnaïve to anti-TNF therapy, 4) is associated with OmpC+, ANCA-−serological factors, and 5) is associated with RNASET2 risk SNPsrs9355610, rs1819333, rs2149085.

Example 3

TNFSF15 and the protein it encodes TL1A, is associated with IBD and arekey mediators of mucosal inflammation. In IBD patients, elevated TL1Alevels correlate with disease severity and genotype. TL1A mediatesmarked enhancement of IFN-γ production. TL1A response biomarkers wereidentified by RNAseq and verified by qPCR in T cells isolated from IBDpatients (20 Crohn's [CD], 20 ulcerative colitis [UC]) compared tonormal (NL). An additional cohort of samples from NL and IBD patientswas used to validate and measure expression/methylation quantitativetrait loci (eQTL/mQTL) in the context of GWAS. RNAseq expressionclustering differentiated TL1A treated versus non-treated cells.RNASET2, a gene encoding an extracellular T2 RNase, was down-regulatedfollowing TL1A treatment. Previous studies associated RNASET2 withsusceptibility for CD. RNASET2 expression in CD patients was lower in“severe” vs. mild disease, i.e., multiple disease flare-ups (p<0.009),medically refractory (p<0.024). Disease risk allele for RNASET2rs1819333 (p=0.015) and TNFSF15 allele associated with enhanced TL1Aexpression, rs6478108, rs6478109 and rs7848647 (p=0.01) were correlatedwith decreased RNASET2 expression. Moreover, siRNA silencing of RNASET2enhanced TL1A mediated IFN-γ secretion. Without being bound to anyparticular theory, the inventors believe that down-regulation of RNASET2is a hallmark of TL1A driven severe CD.

RNASET2 expression and DNA methylation were examined in a separatecohort of freshly isolated un-stimulated T cells from NL, CD or UCpatients. Methylation at RNASET2 locus inversely correlated with mRNAexpression. eQTL of RNASET2 alleles was associated with decreasedexpression. Significantly enhanced RNASET2 methylation was observed inCD patients with severe disease requiring surgical intervention (Table14). No correlation was observed in NL or patients with mild disease.Likewise, increased RNASET2 methylation was associated with TNFSF15 riskalleles associated with enhanced TL1A expression (Table 14).Epigenetically, the RNASET2 eQTL/mQTL region overlaps with histoneH3K4me3 and H3K27ac and DNase HS activation sites. This regionco-localizes with transcription factor binding for NFκB, jun, ATF3 andCEBPD—all of which are up-regulated in response to TL1A treatment. Theresults identify RNASET2 as a TL1A response gene involved in regulationof IFN-γ production. In CD patients with severe disease there ishyper-methylation and decreased expression of RNASET2, which may bereflective of prior exposure in-vivo to TL1A. Thus, without being boundto any particular theory, the inventors believe that RNASET2 serves as anovel potential disease severity biomarker to identify a subset of CDpatients most likely to benefit from anti-TL1A therapy.

TABLE 14 Increased RNASET2 methylation associated with TNFSF15 riskallele. RNASET2 TNFSF15 p value rs62436418 rs2236313 rs2769345 rs1819333rs9355610 rs6478108 rs6478109 rs7848647 eQTL 0.013 0.024 0.038 0.0380.011 na na na mQTL 0.001 2.7 × 10⁻¹³ 2.7 × 10⁻¹³ 2.7 × 10⁻¹³ 1.4 × 10⁻⁹0.005 0.013 0.003 (RNASET2)

The inventors further analyzed 3 cohorts of patients including 11 UCCD3⁺ PBT (medically refractive), 43 CD CD3⁺ PBT (23 were medicallyrefractive and 20 were mild) and 17 normal CD3⁺ PBT. The samples wererun on the Infinium 450 Methylation Array and 11 CD, 12 UC and 4 NLsamples were run on the Infinium Expression Array. The inventorsdemonstrate that RNASET2 expression is decreased following TL1Atreatment of CD4⁺ T cells and that silencing of RNASET2 enhances TL1Amediated IFN-γ secretion.

TABLE 15 Clinical Features Expres- Methyla- RNASET2 sion tion Multipledisease flares

Refractive disease requiring surgical intervention

Patients naïve to anti-TNF therapy

RNASET2 risk allele SNPs rs9355610, rs1819333,

rs62436418, rs22236313, rs2769345 RNASET2 risk allele SNPs Refractivedisease

Normal or Mild disease

Epigenetic studies demonstrated that RNASET2 eQTL/mQTL region overlapswith epigenetic activation sites for 1) histone H3K4me3 and H3K27ac, 2)DNase HS, 3) co-localizes with transcription factor binding for NFkB,jun, ATF3 and CEBPD, all of which are up-regulated in response to TL1Atreatment. Furthermore, the enhancer element in primary T memory cellsfrom peripheral blood, the DNAse HS site in CD4⁺ naïve T cells and theeQTL RPS6KA2 monocytes were linked to the rs1819333 allele.

Example 4

TL1A synergizes with IL-12/IL-18 resulting in a rapid (within 6-8 hours)and marked enhancement of IFN-γ expression. RNAseq analysis was used toidentify the TL1A response genes regulating IFN-γ expression. Twentygenes were differentially expressed (at least 2-fold) in TL activatedtotal CD4+ T cell population. This can be largely due to the fact thatIFN-γ secreting T cells constitute only a very small subset (1-3%) ofthe total CD4+ T cell population (FIG. 15). CD4 T cells from healthydonors were treated with IL12/IL18 and TL1A for 8 hours and then sortedinto IFN-γ-secreting and non-secreting subsets (FIG. 15) andwhole-genome transcriptional analyses (GWAS) of mRNA was performed.Unsupervised hierarchical clustering of the entire 8075 expressed geneset clearly distinguished between the TL1A mediated IFN-γ-secreting andnon-secreting subgroups (FIG. 16).

A class prediction analysis classifying the IFN-γ-secreting andnon-secreting subgroups based on expression levels was performed. Thebest predictor transcript list consisted of 764 genes with at least twofold differential expression between the IFN-γ secreting subset(p-value<0.00005) (FIG. 17). Gene ontology analysis showed that thedifferentially expressed genes were enriched for those in pathwaysassociated with proteasome, apoptosis, RNA expression and T cellreceptor signaling, and were downstream targets of Infliximab(activation z score=−4, p value=2e-15). GWAS has identified multiple IBDrisk variant SNPs. There was a significant increase in the proportion oftranscripts located within 0.5 MB from an IBD risk SNPs (14% vs. 9%, pvalue=3.3e-6) compared to proportion of predictor genes in otherregions. In fact, differentially expressed transcripts mapped to 34% ofall IBD risk associated regions (FIG. 18). Without being bound to anyparticular theory, the data demonstrate a strong contribution for thesegenes not only in TL1A mediated modulation of IFN-γ expression but ascontributing factors modulating IBD susceptibility and pathogenesis.

A volcano plot visualizing the significance and magnitude ofdifferentially expressed predictor transcripts associated with IBD riskloci, allowed us to prioritize candidate genes (FIG. 20). Of thesegenes, TL mediated expression of IFN-γ was confirmed to be mostsignificantly up-regulated and RNASET2 as most significantlydown-regulated (FIG. 20). RNASET2, a member of the Rh/T2/S family ofribonuclease, was the only IBD risk associated gene displaying a greaterthan 5 fold TL1A mediated down-regulation in expression. RNASET2 hasbeen identified by GWAS as a potential IBD risk gene. As the functionalrole of RNASET2 in IBD pathogenesis was unknown, the regulation ofRNASET2 expression in IBD was examined. Without being bound to anyparticular theory, the inventors believe that since RNASET2 is a ‘classpredictor’ gene, differential expression can be detected in total CD4+ Tcells. Resting or IL12/IL18 treated CD4+ T cells from CD, UC patients orNL controls were isolated and RNASET2 levels were compared in thepresence or absence of TL1A for 8 hours. As seen in FIG. 7, in contrastto what we had been observed in cells from NL donors, IBD patients didnot display a TL1A mediated decrease in RNASET2 expression levels.Rather decreased expression levels of RNASET2 were associated in CDpatients with “severe” compared to mild disease course. RNASET2expression was significantly lower in cells isolated from CD patientsexhibiting multiple disease flares per year (p<0.001) (FIGS. 8A and 8C)and likewise decreased RNASET2 expression was detected in CD patientswho were medically refractive requiring surgical intervention fordisease management (p<0.024) (FIG. 8B). A similar trend was seen in UCpatients.

Gene expression quantitative trait (eQTL) was performed to characterizethe functional correlation between RNASET2 gene variation and the genetranscript expression level. The IBD risk SNP tagging in Caucasians,rs1819333, and rs2149085 identified in the CD Korean population, areboth located within −3.5 kb from the transcriptional start site, withinthe RNASET2 promoter region. An additional promoter SNP, rs9355610, hasbeen shown to be associated with susceptibility with Grave's autoimmunethyroid disease. In peripheral cells isolated from CD patients theRNASET2 disease risk alleles rs1819333 (p=0.015) and rs2149085(p=0.015), as well as, rs9355610 (p=0.04) display eQTL and werecorrelated with decreased RNASET2 expression (FIG. 9). Without beingbound to any particular theory, the data indicates a pathway wherebydown-regulation of RNASET2 alters IFN-γ expression. The functional roleof RNASET2 in regulation of IFN-γ expression was confirmed using siRNAmediated silencing. CD4+ T cells were transfected with siRNA targetingRNASET2 mRNA or control siRNA and then treated with IL12/IL18 and TL1A.The expression of RNASET2 mRNA itself displayed a 60-70% inhibition byRNASET2 siRNA (FIG. 21A). In parallel, a significant enhancement (>1.5fold) in IFN-γ expression was seen in cells transfected with RNASET2siRNA compared to control scrambled siRNA (FIG. 21B).

Without being bound to any particular theory, the inventors believe thatconsidering the pivotal role of IFNγ in pathogenesis of Crohn's diseasethese data collectively indicate that down-regulation of RNASET2 mayserve as a biomarker of TL1A driven severe CD. RNASET2 expression wasexamined in a separate cohort of freshly isolated unstimulated T cellsfrom NL, CD and UC patients. Since DNA methylation impacts upon geneexpression and since most disease-risk genetic polymorphisms map outsideof the transcribed exome in regions subject to epigenetic modification,the DNA methylation status of RNASET2 was examined as well. Inunstimulated T cells from CD and UC patients an inverse correlation wasobserved between IFNγ expression levels and RNASET2 (FIG. 22). Moreover,as seen in FIG. 10, there was a significant negative correlation betweenexpression and methylation which was inversely related to distance,mainly within 50 kb upstream and downstream from the transcriptionalstart site (TSS). Additionally, there was a significant overlap betweenIBD disease risk genetic variants and regions correlative formethylation and expression levels (FIG. 10). The strongest correlation(p=8.5×10⁻⁵) was observed at a CpG site (1.4 kb) within the first intron(FIG. 23).

The functional correlation between RNASET2 gene variation and the genetranscript expression level was confirmed in unstimulated peripheral Tcells from IBD patients with refractory disease (FIG. 11), withdecreased expression correlating with the RNASET2 risk allele variantSNP. Moreover, a similar eQTL was observed for mRNA extracted fromtissue obtained from surgical resection of the small bowel using geneexpression microarray (FIG. 12). The correlation between RNASET2 genevariation and methylation, mQTL was also examined and a significant mQTLwas observed with an increase in methylation in IBD patients withrefractory disease (FIGS. 13A-13D). In contrast, no mQTL was detected incells isolated from patients with mild disease or NL subjects.

The role of these genetic variations affecting gene expression (eQTL)and DNA methylation (mQTL) was mapped across all informative SNPsspanning the RNASET2 locus (FIG. 14). In T cells isolated from IBDpatients with medically refractory disease, there is strong overlappingeQTL and mQTL from 10 kb downstream of RNASET2 TSS to −170 Kb upstream,within the CCR6 locus. Likewise, there was a remarkable overlap in eQTLwhen comparing RNSASET2 expression from unstimulated peripheral T cellsto small bowel surgical resection in patients with refractory disease.In contrast, in patients with mild disease or NL subjects no mQTL wasdetected (FIGS. 14A and 14B). This without being bound to any particulartheory, the data suggests that down-modulation of RNASET2 is a componentof TL1A mediated enhancement of IFN-γ expression. Additionally,epigenetic modulation of RNASET2 and reduced gene expression in IBDpatients with a known IBD risk variant SNP is associated with a moresevere course of disease.

Example 5

Methods

Peripheral T cells isolated from NL (normal) donors were cultured withor without TL1A for 8 hours. Gene expression profiling was performed byRNA sequencing (RNA-seq) and quantitative polymerase chain reaction(qPCR) using the subset of interferon gamma (IFN-γ)-producing cellspurified by flow cytometry. Enzyme-linked immunosorbent assay (ELISA)and small interfering RNA (siRNA) inhibition and qPCR were used tomeasure the role of ribonuclease T2 (RNASET2) in TL1A mediatedexpression of IFN-γ. The role of RNASET2 in IBD was investigated usingperipheral T cells isolated from IBD patients (20 CD and 20 UC)stimulated in a similar fashion. Findings were validated usingadditional samples of unstimulated T cells from NL and IBD patients orsmall bowel (SB) surgical resection and analyzed for expressionquantitative trait loci (eQTL) and methylation quantitative trait loci(mQTL) based on genotyping and clinical data.

Screening for predicted motif disruption of transcription factor (TF)binding sites identified candidate regulatory SNPs. Proteomic analysisand measurement of cytokine secretion were used to determine effect ofRNASET2-directed small interfering RNA (siRNA) on protein expression.Cell aggregation was measured by flow cytometry.

Study Subjects

Human subjects were recruited through the MIRIAD IBD Biobank at the F.Widjaja Foundation Inflammatory Bowel and Immunobiology ResearchInstitute at Cedars-Sinai Medical Center. All control subjects werehealthy individuals, free of medication, and with no known personal orfamily history of autoimmune disease or IBD. Informed consent (approvedby the Institutional Review Board at Cedars-Sinai Medical Center) wasobtained from all participating subjects. IBD patients were defined as“refractory” if surgical intervention was required for diseasemanagement following failure of medical therapy. IBD patients weredefined as “mild” if they had no prior surgeries and no active diseaseat time of sample collection. CD patients exhibiting one or more diseaseflares per year were defined to have “severe disease” compared topatients with no disease flares per year. Clinical characteristics wereprospectively collected from 564 CD patients who had undergone surgicalresection.

Isolation of Lymphocyte Populations

Peripheral blood mononuclear cells (PBMC) were isolated from healthyvolunteers by separation on Ficoll-Hypaque gradients. CD3⁺ T cells (PBT)were isolated using CD3-immunomagnetic beads (Miltenyi Biotech, Auburn,Calif.) and were at least 95% pure. CD4⁺ T cells were isolated usingnegative selection by depletion with magnetic beads (StemcellTechnologies, Vancouver, BC, Canada) and were at least 95% pure.

Infinium 450K Bead Chip Assay

DNA samples from CD3⁺ T cells were bisulfite converted using the Zymo EZDNA Methylation kit (Zymo Research) with an input of 1 μg. The assay wascarried out as per the Illumina Infinium Methylation instructions, usingthe Infinium HumanMethylation450 BeadChip Kit (Illumina Inc., San Diego,Calif.). Data were visualized and normalized using the GenomeStudiosoftware. The methylation β values were recalculated as the ratio of(methylated probe signal)/(total signal).

IFN-γ Assay

IFN-γ was measured by an amplified ELISA. Greiner Bio-One (Longwood,Fla.) ELISA plates were coated overnight with 100 μl of 5 μg/mlmonoclonal anti-IFN-γ (BD Biosciences, Woburn, Mass.). Samples andstandards were added for 24 h followed by addition of 100 μl of 2.5μg/ml polyclonal biotinylated rabbit anti-IFN-γ (BD Biosciences) for 2h. This was followed by addition of 100 μl of 1/1000 diluted alkalinephosphatase-conjugated streptavidin (Jackson ImmunoResearchLaboratories, West Grove, Pa.) for 2 h. Substrate, 0.2 mM NADP(Sigma-Aldrich, St. Louis, Mo.) was added for 30 min followed byaddition of amplifier (3% 2-propanol, 1 mM iodonitrotetrazolium violet,75 μg/ml alcohol dehydrogenase, and 50 μg/ml diaphorase; Sigma-Aldrich)for 30 min. Plates were read at 490 nm using an E max plate reader(Molecular Devices, Sunnyvale, Calif.).

Gene Expression Assay for CD3⁺ T Cells

Expression analysis of CD3⁺ T cells was performed using the Illuminagenome-wide expression BeadChip (HumanHT-12_V4_0_R2) (Illumina) or Nugenhuman FFPE RNA-seq library system. Illumina Gene expression data wereprocessed using the BRB array tools and the lumi package in R. The datawere log₂-transformed and normalized using robust spline normalization.Libraries for RNA-Seq were prepared with Nugen human FFPE RNA-seqlibrary system. The workflow consists of cDNA generation, fragmentation,end repair, adaptor ligation and PCR amplification. Different adaptorswere used for multiplexing samples in one lane. Sequencing was performedon Illumina NextSeq 500 for a single read 75 run. Data quality check wasdone on Illumina SAV. Demultiplexing was performed with IlluminaBcl2fastq2 v 2.17 program. The reads were first mapped to the latestUCSC transcript set using Bowtie2 version 2.1.0 and the gene expressionlevel was estimated using RSEM v1.2.15. FPKM was used to normalize thegene expression.

siRNA Inhibition and Quantitative Proteomic Analysis

Freshly isolated CD4⁺ T cells (15×10⁶) were cultured overnight in RPMI1640 medium containing 10% fetal calf serum, washed, resuspended in 250fresh medium, and electroporated in the presence of 150 pmole of RNASET2siRNA or control siRNA (600 V, for 9 pulses of 500 μsec, with 100 μsecbetween pulses) using 4 mm (gap width) cuvettes in a BTX Electro SquarePorator ECM 830 (Genetronics, Inc., San Diego, Calif.). Sequences usedin siRNA inhibition are depicted in Table 16.

TABLE 16 siRNA sequences SEQ Sequence Name Sequence ID NORNASET2 siRNA-sequence forward 5′-GCAAGAGAAAUUCACAAACUGCAGC-3′  7RNASET2 siRNA-sequence reverse 5′-GCUGCAGUUUGUGAAUUUCUCUUGCUU-3′  8Control siRNA-sequence forward 5′-CUUCCUCUCUUUCUCUCCCUUGUGA-3′  9Control siRNA-sequence reverse 5′-UCACAAGGGAGAGAAAGAGAGGAAGGA-3′ 10

Tandem mass tagging (TMT)-based quantitative proteomics analysis wasconducted as described (Qu et al., Sci Rep 2016; 6:32007). For eachsample, 50 μg proteins were digested in parallel into tryptic peptidesusing filter-aided sample preparation (FASP) (Wisniewski et al., Nat.Methods 2009; 6:359-62). Peptides derived from eight samples and apooled internal standard were labeled with a set of TMT10plex reagents(Thermo Scientific), mixed, desalted, separated into 24 fractions byhigh-pH liquid chromatography, and concatenated into 8 fractions.Fractionated peptides were resolved on a 50 cm EASY-Spray analyticalcolumn, and analyzed by an LTQ Orbitrap Elite mass spectrometer (ThermoScientific) in the data-dependent acquisition mode, using thehigher-energy collisional dissociation (HCD) method for tandem massspectrometry. Acquired raw data were searched against the human Uniprotdatabase (released on Oct. 17, 2015, containing 20,982 sequences) withProteome Discoverer (v2.1), using the SEQUEST algorithm. A stringent 1%false discovery rate was set to filter peptide and proteinidentifications. Peptides with >30% precursor ion interference wereexcluded from protein quantification.

Flow Cytometry and Analysis of Cellular Aggregation

IFN-γ-secreting CD4⁺ T cells was isolated by flow cytometry followingactivation of cells with recombinant human IL-12 (500 pg/ml, R&DSystems, Minneapolis, Minn.) and IL-18 (50 ng/ml, R&D Systems) and TL1A(100 ng/ml, Fitzgerald Industries International, Acton, Mass.) for 8 h.IFN-γ-secreting CD4+ T cells were detected using an IFN-γ secretionassay cell enrichment and detection kit (Miltenyi Biotec, San Diego,Calif.). Cells were sorted on a FACS Aria II (BD Biosciences, San Jose,Calif.).

Intracellular IFN-γ production and analysis of cellular aggregation wasconducted essentially as described (Dezorella et al., Cytometry B ClinCytom 2016:90:257-66) Briefly, cells were either rested or stimulatedfor 24 h with IL12/IL18 and TL1A and Berfeldin A (10 ug/ml) was addedfor the last 4 h. Cells were fixed with 4% paraformaldehyde,permeabilized with 0.1% Triton X-100 and 0.2% saponin and stained forintracellular IFN-γ (brilliant violet 421-IFN-γ, eBioscience) or isotypecontrol. Samples were washed and stained for cellular aggregation(propidium iodide). Cells were acquired on a CyAn™ ADP Flowcytometer(Dako, Carpinteria, Calif., USA) and analyzed with FlowJosoftware(TreeStar Inc., Ashland, Oreg., USA). For LFA1 blocking analysis cellswere pre-incubated overnight in conical microplates with monoclonalcontrol mouse IgG1k (15 ug/ml) or anti-LFA1 (TS1/18) followed bystimulation with IL12, IL18 and TL1A for 24 h.

qPCR

Total RNA was isolated using the RNeasy kit (Qiagen, Inc., Valencia,Calif.) and gene expression was measured by real-time quantitativeRT-PCR. Five hundred nanograms of total RNA were used in each RT-PCRreaction, with oligo (dT) (Integrated DNA Technologies) as primer, usingthe Omniscript kit and protocol (Qiagen). Real-time PCR was performedusing a Mastercycler® ep realplex PCR detection system (Eppendorf,Hauppauge, N.Y.). PCR assays were run in duplicate. Primer sequences(Integrated DNA Technologies) spanned introns and are depicted in Table17.

TABLE 17 Primer sequences SEQ ID Sequence Name Sequence NO IFN-γ forward5′-TTGGGTTCTCTTGGCTGTTACT-3′ 11 IFN-γ reverse5′-ATCCGCTACATCTGAATGACCTG-3′ 12 RNASET2 5′-CTTCCTTGCAGGACTCACCAC-3′ 13forward RNASET2 5′-GCTGATGTGAAGGTGCAAACTC-3′ 14 reverse ACTB forward5′-CGTGCTGCTGACCGAGG-3′ 15 ACTB reverse 5′-AAGGTCTCAAACATGATCTGGGT-3′ 16Genotyping

Genotype data was obtained for Caucasian subjects using IlluminaHumanImmuno BeadChip array. Markers were excluded based on: test ofHardy-Weinberg Equilibrium with significance threshold of p≤10⁻³; ifgenotyping rate was <100% (for eQTL and mQTL associations) or <98% (forGWAS) and if minor allele frequency was <5%. Identity-by-descent wasused to exclude related individuals (Pi-hat scores >0.25) using PLINK.ADMIXTURE was used to perform ethnicity analysis to get ethnicityproportion estimation for individuals. An individual with Caucasianproportion ≥0.75 was classified as Caucasian. Independent Caucasiansamples were identified based on relatedness check (using cut-off pi-hatscores) and ethnicity analysis from admixture and all subsequentassociations were performed using these samples. Principal components ingenotype data for independent Caucasian samples were generated usingTRACE. LDHeatmap R package was used to generate LD plot for the SNPs inRNASET2 locus using genotype data for 139 subjects. Details of the QCand genotyping in IIBDGC cohort can be found in previous reports(Jostins et al., Nature 2012; 491:119-24 and Liu et al., Nat Genet 2015;47:979-86). In brief, 18,602 CD cases and 33,938 non-IBD controlsgenotyped using ImmunoChip were included in the analysis after sampleswith >5% missing data, samples of non-European ancestry from populationstratification or with abnormal mean intensity values, and SNPs with >2%missing data or HWE p-value <10⁻¹⁰ in controls were removed. Of the CDcases from IIBDGC, 13,511 have disease behavior information collectedbased on Montreal classification as reported previously (Cleynen et al.,Lancet 2016; 387:P156-67) (described as B1, non-stricturing,non-penetrating, B2, stricturing and B3, penetrating diseases).

Expression Data for Small Bowel Surgical Samples

Single channel microarray expression data extracted using Agilentfeature extraction software were received from Genome Technology AccessCenter at Washington University, St. Louis. Raw expression dataavailable in technical duplicates were normalized using LIMMA packageimplemented in R version 3.2.2. The expression data preprocessingincluded background correction of the expression data, followed by log2-transformation and quantile-normalization.

EQTL and mQTL Mapping

eQTL and mQTL mapping was implemented in Matrix eQTL R package. Forsmall bowel surgery samples, eQTL mapping was done using independentCaucasian samples (n=85). Associations between genotype and probeexpression level (for eQTL) or methylation β values (for mQTL) wereperformed using a linear regression model with additive genotypeeffects. All associations were conducted with gender and first twoprincipal components in genotype data as covariates along with genotype.Around 200 genetic variants within 200 KB of RNASET2 TSS were used toperform associations with RNASET2 gene expression or methylation levels.

Motif Analysis and Identification of Candidate Regulatory SNPs

All variants exhibiting eQTL and mQTL were analyzed for predicteddisruption of TF binding motifs using the bioconductor motifbreakRpackage (Coetzee et al., Bioinformatics 2015; 31:3847-9). Only T cellspecific TFs identified as being expressed using RNAseq data from CDpatients, were carried forward. Candidate regulatory SNPs were thenanalyzed for potential functionality based on Roadmap EpigenomicsMapping Consortium (REMC) data (Roadmap Epigenomics C. et al, Nature2015; 518:317-30). Potential active enhancer regions were determinedbased on overlap of the histone modification H3K4me1 with H3K27acsignals (Coetzee et al., Hum Mol Genet 2015; 24:3595-607). Potentialfunctionality of TF regulation was determined based on REMC CHIP-seqbinding signal and Regulome data.

Pathway Analysis

Pathway analysis was accomplished through the use of Qiagen's Ingenuity®Pathway Analysis (IPA®, Qiagen, Redwood City, www.qiagen.com/ingenuity)and The Database for Annotation, Visualization and Integrated Discovery(DAVID, http://david.abcc.ncifcrf.gov).

Statistical Analysis

Modeling, data analysis, and data mining were performed using the BRBarray tools (brb.nci.nih.gov/BRB-ArrayTools) and R-program (version2.2.2; www.r-project.org). Class prediction analysis used compoundcovariate predictor, diagonal linear discriminant analysis, k-nearestneighbor (using k=1 and 3), nearest centroid, and support vectormachines, based upon a minimum p value of 0.001. Cluster analysis wasperformed using Cluster 3.0 and Java Treeview 1.1.6r4. Tests forstatistical significance were determined using JMP Statistical Software(Cary, N.C.). Test for clinical association between of rs1819333 andrs9355610 SNPs and therapeutic failure, ANCA sero-positivity, resectedbowel length and time to reoperation were calculated by parametricStudent's T test and Pearson correlation; test of association and trendusing Fisher's exact test and Kaplan-Meier Survival Curves. Associationwith endoscopic recurrence was calculated by Cochran-Armitage trendtest.

Results

In this study, the inventors identified down-modulation of RNASET2, anIBD susceptibility gene, as a component of TL1A-mediated enhancement ofcytokine production and as a novel potential biomarker of diseaseseverity. Down-regulation of RNASET2 following siRNA silencing resultedin increased IFN-γ secretion, without being bound to any particulartheory, supporting a role in regulating inflammatory response. Adecrease in RNASET2 expression was also observed in peripheral T cellsfrom CD patients with one or more yearly disease flares compared topatients with no yearly disease flares. Functionally, quantitative traitloci were associated with RNASET2 disease-risk variants for decreasedexpression (eQTL) in peripheral and mucosal tissues and DNAhypermethylation (mQTL) from CD patients with medically refractory, butnot mild disease. Additionally, RNASET2 disease-risk variants wereassociated with an increase in development of stricturing/penetratingdisease behavior. Furthermore, RNASET2 disease-risk variants wereassociated with a complicated/resistant CD phenotype defined in part bytherapeutic drug failure, ANCA sero-positivity, increased length ofintestinal resection, shorter time to reoperation and post-operativeendoscopy with a high (>2) Rutgeerts score. Motif screening of RNASET2disease-risk variants identified rs2149092 with predicted disruption ofa consensus ETS-TF binding site located within a potential enhancerregion, providing insight into RNASET2 cis-regulatory elements. RNASET2correlated with expression of multiple ETS-transcription factors.Finally siRNA silencing of RNASET2 resulted in enhanced IFN-γ, increasedICAM1 and concomitant T cell aggregation while anti-LFA1 blocking ofaggregation suppressed IFN-γ secretion.

Identification of Differential Gene Expression Associated withTL1A-Mediated Enhancement of IFN-γ Production

To identify the underlying molecular pathways involved in TL1A-mediatedenhancement of IFN-γ production, a key IBD proinflammatory cytokine,CD4⁺ T cells were treated with TL1A, sorted into IFN-γ-secreting andnon-secreting subsets and analyzed by RNA-seq (FIG. 15 and FIG. 27).Unsupervised hierarchical clustering of the set of expressed genesclearly distinguished TL1A-mediated IFN-γ-secreting and non-secretinggroups (FIG. 16). Seven hundred and sixty-four “predictor” genes with atleast two-fold differential expression between the IFN-γsecreting/non-secreting subsets (p value <1×10⁻⁵) (FIG. 17) wereidentified. Gene ontology analysis indicated that differentiallyexpressed genes were enriched in pathways associated with T cellreceptor signaling, apoptosis, and RNA expression, and were downstreamtargets of infliximab, an anti-TNF biologic drug. Predictor genes weresignificantly enriched in regions flanking GWAS identified IBDsusceptibility variants (0.25 MB upstream or downstream of the singlenucleotide polymorphism (SNP) compared to other regions (14% vs. 9%, pvalue is 3.3×10⁻⁶, hypergeometric test). Without being bound to anyparticular theory, these data suggest that these genes contribute notonly to TL1A-mediated modulation of IFN-γ expression, but also overlapwith IBD risk-associated loci. Of the IBD-risk associated predictorgenes, expression of IFN-γ was confirmed as the most significantlyupregulated and RNASET2 as the most significantly down regulated gene(FIG. 20). RNASET2 was the only IBD risk associated gene with greaterthan 5-fold down regulation in the IFN-γ secreting CD4⁺ subset.

RNASET2 Regions Displaying Inverse Correlation of Expression and DNAMethylation Levels Overlap with Regions Flanking Disease-Risk AssociatedVariants

RNASET2 is the only human member of the Rh/T2/S family of ribonucleasesand its expression is decreased in ovarian cancer, melanoma andnon-Hodgkin lymphoma. Considering the key role for IFN-γ in pathogenesisof Crohn's disease/IBD, without being bound to any particular theory,these data collectively suggest that down regulation of RNASET2identifies TL1A mediated ‘severe’ CD. RNASET2 expression was examined infreshly-isolated, unstimulated peripheral CD3⁺ T cells from a separatecohort of NL, CD and UC patients. Since DNA methylation is understood tobe one of the mechanisms that impacts gene expression, particularly indisease-associated genetic variants that map outside transcribed exomes,we examined the DNA methylation status across the RNASET2 locus. RNA-seqanalysis demonstrated there was an inverse correlation between TNFSF15expression levels and RNASET2 in peripheral T cells from two independentcohorts comprised of a combined 138 CD patients (FIGS. 24A and 24D).These results were consistent even when each cohort was analyzedseparately (FIGS. 24B and 24C). Moreover, there was a significantnegative correlation between expression and methylation (FIG. 23),mainly within 50 kb upstream and downstream from the transcriptionalstart site (TSS) (FIG. 26). The strongest correlation of methylation andexpression (p=8.5×10⁻⁵) was observed at a CpG site (1.4 kb) within thefirst intron of RNASET2 (FIG. 26). Additionally, CD disease genetic riskvariants, including the IBD risk SNP tagging the RNASET2 locus inEuropean ancestry populations, rs1819333, overlapped with regionscorrelative for methylation and expression levels (FIG. 10).

RNASET2 Disease-Risk Alleles are Associated with Decreased RNASET2Expression and Increased DNA Methylation in CD Patients with RefractoryDisease

Gene expression quantitative trait (eQTL) was performed to characterizethe functional correlation between RNASET2 gene variation and the genetranscript expression level. The disease associated SNPs for IBD risk inEuropeans, rs1819333, and Koreans, rs2149085, as well as the risk SNPassociated with Graves' disease, rs9355610, are located −13 kb from thetranscriptional start site of RNASET2. The functional correlationbetween RNASET2 IBD-risk genotypes and the gene transcript expressionlevels were established in unstimulated peripheral CD3⁺ T cells isolatedfrom IBD patients with refractory disease. The data demonstratedsignificantly decreased RNASET2 expression in T cells from subjectscarrying the RNASET2 risk alleles rs2149085, rs1819333, and rs9355610(FIG. 11). These findings were confirmed with significant eQTL observedfor mRNA extracted from uninflamed small bowel tissue obtained from CDsubjects at surgical resection (FIG. 12). The correlation betweenRNASET2 gene variation and methylation, mQTL was also examined. Asignificant mQTL was observed with an increase in methylation in CDpatients with refractory disease (FIGS. 13A and 13C). In contrast, nomQTL was detected in cells isolated from CD patients with mild diseaseor NL subjects (FIGS. 13B and 13D). Moreover, there was a significantincrease of complicated disease behavior, stricturing/penetratingphenotype (Montreal classification B1 vs. B2 and B3), associated with CDpatients carrying the RNASET2 disease risk SNPs (rs1819333/rs2149085p=0.05, rs9355610 p=0.01).

Gene expression (eQTL) and DNA methylation (mQTL) was mapped across allinformative SNPs spanning the RNASET2 locus (LD plot). In T cellsisolated from patients with medically refractory disease, there isstrong overlapping eQTL and mQTL from 10 kb downstream of RNASET2 TSS to−170 kb upstream, spanning fibroblast growth factor receptor 1 oncogenepartner (FGFR1OP) to the first intron of chemokine (C—C motif) receptor6 (CCR6). Likewise, there was overlap in eQTL when comparing RNASET2expression from unstimulated peripheral T cells to small bowel surgicalresection in CD patients with refractory disease. In contrast, few mQTLassociations were detected in CD patients with mild disease or NLsubjects (FIGS. 14A and 14B). No eQTL association was detected forFGFR1OP or CCR6. These data were further validated in a separate cohortof peripheral T cells isolated from CD patients with medicallyrefractory disease. There was significant overlap between RNASET2 riskvariants associated with CD and corresponding eQTL (FIG. 28) which,without being bound to any particular theory, suggest a functional rolefor RNASET2 in mediating disease.

Attenuated Expression of RNASET2 in CD

To establish a role for RNASET2 in IBD pathogenesis, regulation ofRNASET2 expression in CD4⁺ T cells isolated from IBD patients wasexamined and compared to normal (NL) donors in the presence or absenceof TL1A. As seen in FIG. 7, NL donors, but not IBD patients, exhibited aTL1A-mediated decrease in RNASET2 expression levels. Instead, decreasedexpression levels of RNASET2 were found in CD patients with more severedisease (exhibiting one or more disease flares per year) compared topatients with no yearly disease flares (FIGS. 8A and 8C).

RNASET2 Disease-Risk Alleles are Associated with Complicated andResistant Disease Behavior

To evaluate the association between RNASET2 and disease activity andseverity the inventors utilized a cohort of 564 CD patients who hadundergone surgical resection and were then followed prospectively.Clinical characteristics including indication for surgery were assessedfor association with RNASET2 risk variants (rs1819333 and rs9355610).RNASET2 disease risk variant SNPs were associated with a complicatedstricturing/penetrating phenotype (Montreal classification B1 vs. B2 andB3), (Table 18). At the time of surgery, patients with RNASET2 diseaserisk variant SNPs were associated with therapeutic failure of thiopurineor anti-TNF therapy, ANCA sero-positivity (a marker associated with lackof response to anti-TNF therapy), and an increased length of intestinalresection characteristic attributed to overall disease severity (Table18 and FIGS. 38-39). No association was observed for therapeutic failureon steroids or sulfasalazine. Moreover, patients with RNASET2 diseaserisk variant SNPs who required multiple resections for diseasemanagement exhibited a shorter time to reoperation (FIG. 32).

TABLE 18 Clinical disease parameters associated with RNASET2 riskvariants. rs1819333 rs9355610 Clinical parameter p OR p OR DiseaseBehavior B2 vs. B1^(a) ns ns 0.041 1.07 B3 vs. B1^(a) ns ns 0.056 1.06B2, B3 vs. B1^(a) 0.051 1.05 0.016 1.07 Therapeutic failure ofthiopurine^(b) 0.009 1.68 0.019 1.75 Therapeutic failure of anti-TNF^(b)0.039 1.46 0.042 1.56 ANCA sero-positivity^(b) 0.009 2.24 0.047 2.07Resected segment >30 cm^(b) ns ns 0.004 2.13 >40 cm^(b) ns ns 0.031 1.96Endoscopic recurrence Rutgeert's score 3-4 vs 1-2 p z score p z score Noprophylactic meds^(b) 0.025 2.24 0.024 2.25 ^(a)IIBDGC cohort CD (n =3345)/case control (n = 6277) ^(b)CD patients (n = 584) who hadundergone surgical resection and followed prospectively.

Likewise, RNASET2 risk SNPs were associated with a more severe diseaserecurrence. Post-operative endoscopies revealed an association ofRNASET2 risk SNPs in patients classified with a high Rutgeerts score(>2) who were not receiving postoperative prophylaxis (Table 18). Noassociation was observed for clinical recurrence. Decreased expressionof RNASET2 was also associated with a penetrating disease phenotype(FIG. 31) and ASCA sero-positivity (FIG. 30). Without being bound by anyparticular theory, this data supports an association of RNASET2 diseaserisk SNPs with clinical parameters suggestive of complicated andresistant disease behavior.

RNASET2 Variant in LD with Disease-Tagging SNP Disrupts ETSTranscription Factor Binding Motif

The data presented above demonstrate significant overlap between morethan a hundred CD RNASET2 risk variants, many in linkage disequilibrium,associated with eQTL and mQTL creating difficulty in determiningfunctionality/causality. Since the majority of RNASET2 risk variantsassociated with CD are located in non-coding regions, it is likely thatthese SNPs alter expression through modulation of regulatory functions.Furthermore, without being bound to any particular theory, studiessuggest that SNPs associated with disease often exist within activeenhancer regions of cell types relevant to disease and can disrupt TFbinding motifs. REMC data demonstrate that the RNASET2 locus is markedin primary T cells, compared to other tissues, by putative activeenhancer histone modifications and active gene expression (FIG. 40). Togain insight into the molecular pathways regulating RNASET2 expressionand prioritize the number of candidate functional SNPs, the inventorsperformed motif analysis to predict TF motif disruptions across all SNPswhich were associated with eQTL/mQTL. Variants disrupting motifs of TFsexpressed in T cells were selected and candidate variants in LD with theRNASET2 disease index SNP rs1819333 were focused on. The rs2049092 SNPdisease risk variant, located −569 bp from the index SNP (LD R2=1), lieswithin the highly conserved TTCC motif, utilized by most ETStranscription factors, and is predicted to disrupt TF binding. Sequenceanalysis demonstrates an overlap of IRF4 and Spi1 binding sites adjacentto a JUN binding site (FIG. 36A). Regulome and REMC data confirm TFoccupancy of ETS1, IRF4 and Spi1 binding in lymphoblastoid cell lines(FIG. 36B) which overlaps with histone modifications indicative of anactive enhancer element. Moreover, there is a strong correlation betweenexpression of RNASET2 with multiple members of ETS and JUN TF (FIGS. 36Cand 41). No correlation was observed for IRF4 (FIG. 41). Without beingbound to any particular theory, these data strengthen the relevance ofRNASET2 expression in the immune compartment and support a functionalrole for ETS and JUN transcription factors in regulating transcriptionof RNASET2.

Silencing of RNASET2 Enhances IFN-γ Secretion Via Upregulation of ICAM1Expression and Homotypic T Cell Aggregation

The functional role of RNASET2 in regulation of IFN-γ secretion wastested using siRNA silencing. CD4⁺ T cells transfected with siRNAtargeting RNASET2 mRNA followed by stimulation with TL1A. Cellstransfected with siRNA targeting RNASET2 displayed a 60-70% inhibitionof RNASET2 expression (FIGS. 21A and 37A), and a parallel significantenhancement (>1.5 fold) in TL1A mediated IFN-γ secretion was seencompared to control siRNA (FIG. 21B and FIG. 37B). Without being boundto any particular theory, these data suggest that down regulation ofRNASET2 modulates IFN-γ expression.

In order to define the signaling pathways involved in this process,proteomic analysis was carried out. Candidate targets were selected onthe basis of exhibiting both modulation of expression following siRNAsilencing of RNASET2 as well as TL1A-mediated differential expressionwhen comparing IFNγ secreting and non-secreting T cells (data fromRNAseq analysis). One of the proteins that was up-regulated in responseto RNASET2 silencing and in the IFNγ secreting compared to non-secretingT cells, was ICAM1 (FIG. 42). ICAM1 was recently identified as an IBDsusceptibility locus, with up-regulated gene expression associated withthe disease-risk variant. ICAM1 is a transmembrane adhesion proteincommonly expressed by vascular endothelium and leukocytes. Binding ofICAM to the LFA1 receptor on T cells facilitates and stabilizescell-cell interactions. Studies have demonstrated increased ICAM1expression on activated T cells and proposed a role for ICAM1-LFA1binding in inducing homotypic T cell aggregation and subsequent T cellsdifferentiation. To examine the effect of cell-cell contact on TL1Amediated IFN-γ secretion, cells were incubated in flat bottom andconical bottom microwells. A greater than 3 fold increase in IFN-γproduction was consistently observed when cells were incubated in closecell-cell conical geometry (data not shown). Flow cytometry was thenused to test the hypothesis that TL1A mediated enhancement of IFN-γproduction is facilitated by homotypic T cell aggregation. Briefly, Tcells were stimulated in the presence or absence of TL1A and thenstained with an antibody for intracellular IFN-γ (FIGS. 37C and 37D,left panels) and for cellular aggregation using propidium iodide (PI)(FIGS. 37C and 37D, upper and lower right panels). The PI-labeled peakscorrespond to number of cells per event allowing for identifying singlecells versus cellular aggregates. The first peak in each histogramcorresponds to single cell events (black brackets) and the successivepeaks, to multicellular aggregates (gray brackets). Only a smallpercentage of the unstimulated T cells secreted IFN-γ, and these cellswere almost equally distributed as single cell events and cellularaggregates (FIG. 37E, left panel). Following TL1A stimulation, there wasa significant increase in both the percentage and size of cellularaggregates (upper right panels of FIG. 37C compared to FIG. 37D, as wellas, the overall number of IFN-γ producing cells (6-fold) (FIGS. 37E and37F) and a 30-fold increase in IFN-γ secretion (data not shown). Incontrast, the majority of T cells that do not produce IFN-γ, arecomprised of single cell events regardless of whether they were culturedwith or without TL1A stimulation (FIG. 37E, right panel). Without beingbound to any particular theory, these results suggest that cellularaggregation may contribute to both an increase in the number of cellsproducing IFN-γ and to overall amount of IFN-γ production, and TL1Astimulation may enhance this process. The functional role of TL1A inmediating cellular aggregation via ICAM1-LFA1 engagement was testedusing an LFA-1 blocking antibody. As seen in FIG. 37G, there was anoverall 43% reduction in IFN-γ secretion in response to blocking LFA-1engagement, compared to IgG control antibody (p value=0.047). Withoutbeing bound to any particular theory, taken together these data indicatethat TL1A-mediated downregulation of RNASET2 and concomitant enhancementof ICAM1 expression, promotes homotypic T cell aggregation andaugmentation of IFN-γ production. It is noted that an increase inexpression of ICAM1 was associated in CD with ASCA sero-positivity andpre-op therapeutic failure of anti-TNF and thiopurine (FIG. 43),clinical parameters associated with decreased RNASET2 and diseaseactivity.

Example 6

Both RNASET2 and TNFSF15 have been identified among the 201 GWAS IBDsusceptibility loci. TL1A, the protein encoded by TNFSF15, is a keymediator of mucosal inflammation. Elevated TL1A levels correlate withTNFSF15 genotype and disease severity. The inventors have identifiedthat TL1A down regulates expression of RNASET2 in T cells. TNFSF15 andRNASET2 expression is inversely correlated in T cells from CD patients(p=5×10⁻¹⁶). The potential of RNASET2 as an IBD prognostic biomarker wasexamined.

The role for RNASET2 disease associated SNPs in IBD was analyzed byexamining expression and methylation quantitative trait loci (eQTL/mQTL)in peripheral T cells from patients undergoing surgery (n=21) and smallbowel surgical samples (n=85). CD patients (n=584) who had undergonesurgical resection were followed prospectively. Clinical characteristicsincluding indication for surgery were assessed for association withRNASET2 risk variants (rs1819333 and rs9355610).

RNASET2 disease associated SNPs were correlated with decreased RNASET2expression (eQTL) in peripheral and mucosal tissues (p<0.001) and DNAhypermethylation (mQTL) (p<0.001) in patients requiring surgicalintervention for disease management compared to those who wereresponsive to IBD therapeutics (n=16). RNASET2 disease associated SNPswere associated with therapeutic failure of thiopurine (p=0.02, OR=1.7)or anti-TNF therapy (p=0.04, OR=1.59), ANCA sero-positivity (a markerassociated with lack of response to anti-TNF therapy) (p=0.02, OR=2.27),and an increase in overall length of intestinal resection (>30 cmp=0.004, OR=2.13/>40 cm p=0.03, OR=1.96). Patients with RNASET2 diseaseassociated SNPs exhibited a shorter time to reoperation (p=0.04, zscore=2.16). Post-operative endoscopies (n=369) with a high Rutgeertsscore (>2) were associated with RNASET2 risk SNPs in patients notreceiving post-op prophylaxis (p=0.02, z score=2.56) or those onanti-TNF therapy alone (p=0.03, z score=2.46), whereas no associationwas detected for patients on other IBD therapeutics.

This study identifies functional consequences of RNASET2 diseaseassociated SNPs that are associated with clinically relevant diseasebehavior. RNASET2 risk SNPs were associated with clinical parameterssuggestive of a complicated and resistant disease behavior. Moreover,response to therapeutics following surgery and recurrence of diseasewere associated with RNASET2 risk SNPs. Without being bound to anyparticular theory, these results taken together with our previousfindings indicate that regulation of RNASET2 may underlie diseasepathology triggered by TL1A and serve as a disease biomarker identifyingsubjects not responsive to current treatment strategies who may benefitfrom alternate therapeutic approaches.

TABLE 19 Clinical features associated with RNASET2 disease risk SNPsrs1819333 rs9355610 CD phenotype at Time of Surgery p OR p ORtherapeutic failure of thiopurine 0.009 1.68 0.019 1.75 therapeuticfailure of anti-TNF 0.039 1.46 0.042 1.59 ANCA sero-positivity 0.0092.24 0.047 2.07 Length of resected segment >30 cm 0.004 2.13 >40 cm0.031 1.96 Family history of disease 0.030 1.58 0.030 1.78 B2 vs B10.041 1.07 B3 vs B1 0.056 1.06 B2, B3 vs B1 0.051 1.05 0.016 1.07 CDpatients (n = 584) who had undergone surgical resection and followedprospectively IIBDGC cohort CD (n = 7173)/case control (n = 6278)

TABLE 20 Endoscopic Recurrence Endo- 3-year clinical scopic recurrencerate score Definition (%) 0 No lesions 5 1 ≤aphtous lesions 5 2 apthouslesions with normal mucosa between 15-20 the lesions, or skip areas oflarger lesions or lesions confined to ileocolonic anastomosis 3 Diffuseapthous ileitis with diffusely 40 inflamed mucosa 4 Diffuse inflammationwith already larger 90 ulcers, nodules, and/or narrowing Adapted fromRemedica Journals Post-op rs9355610 Endoscopic recurrence Rutgeert'sscore 3-4 vs 1-2 p z score No prophylactic meds 0.040 2.25 Anti-TNFalone 0.016 2.69

The rs2149092 (C-non-risk allele/T-risk allele) risk SNP abolishesIRF4/PU.1/ELF-1 binding site. IRF4 is an IBD susceptibility SNP that islymphocyte specific and is essential for the differentiation of Th1,Th2, Th9, Th17 and T reg subsets. ELF-1 is a CD susceptibility SNP inthe Japanese population. It is an ETS family transcription factor thatis expressed in lymphoid cells, acts as both an enhancer and a repressorof expression and is involved in IL2 and IL23 signaling. PU.1 is also anETS family transcription factor and is essential for early stages of Tcell development. It down regulates γδ T Cells which are found in themucosa and plays a role in innate immunity and when expressed in T_(H)9cells, these cells drive T cell-mediated colitis via IL-9 receptorsignaling in intestinal epithelial cells.

RNASET2 expression is decreased following TL1A treatment in IFN-γsecreting CD4⁺ T cells and that silencing of RNASET2 enhances TL1Amediated IFN-γ secretion. Clinical correlates have also been identifiedfor RNASET2 disease associated SNPs, which include, but are not limitedto therapeutic failure of thiopurine therapy, therapeutic failure ofanti-TNF therapy, ANCA Sero-positivity, B2/B3 versus B1(structuring/penetrating vs non-penetrating/non-stricturing) disease, anincrease in length of intestinal resection, decreased time to secondsurgery and endoscopic recurrence of disease with high Rutgeerts score.

Various embodiments of the invention are described above in the DetailedDescription. While these descriptions directly describe the aboveembodiments, it is understood that those skilled in the art may conceivemodifications and/or variations to the specific embodiments shown anddescribed herein. Any such modifications or variations that fall withinthe purview of this description are intended to be included therein aswell. Unless specifically noted, it is the intention of the inventorsthat the words and phrases in the specification and claims be given theordinary and accustomed meanings to those of ordinary skill in theapplicable art(s).

The foregoing description of various embodiments of the invention knownto the applicant at this time of filing the application has beenpresented and is intended for the purposes of illustration anddescription. The present description is not intended to be exhaustivenor limit the invention to the precise form disclosed and manymodifications and variations are possible in the light of the aboveteachings. The embodiments described serve to explain the principles ofthe invention and its practical application and to enable others skilledin the art to utilize the invention in various embodiments and withvarious modifications as are suited to the particular use contemplated.Therefore, it is intended that the invention not be limited to theparticular embodiments disclosed for carrying out the invention.

While particular embodiments of the present invention have been shownand described, it will be obvious to those skilled in the art that,based upon the teachings herein, changes and modifications may be madewithout departing from this invention and its broader aspects and,therefore, the appended claims are to encompass within their scope allsuch changes and modifications as are within the true spirit and scopeof this invention. It will be understood by those within the art that,in general, terms used herein are generally intended as “open” terms(e.g., the term “including” should be interpreted as “including but notlimited to,” the term “having” should be interpreted as “having atleast,” the term “includes” should be interpreted as “includes but isnot limited to,” etc.).

What is claimed is:
 1. A method of treating Inflammatory Bowel Disease(IBD) in a subject, the method comprising administering atherapeutically effective amount of a therapeutic agent to the subject,provided a single nucleotide polymorphism (SNP) at rs2149092 comprisinga “T” at a nucleoposition 501 within SEQ ID NO: 2 is detected in asample obtained from the subject.
 2. The method of claim 1, provided aSNP at rs1819333 comprising an “A” allele at a nucleoposition 501 withinSEQ ID NO: 1 is detected in the sample obtained from the subject.
 3. Themethod of claim 1, wherein the IBD is severe IBD characterized by atleast one of a therapeutic failure of an anti-Tumor Necrosis Factoralpha (TNFa) therapy, multiple flare-ups per year, stricturing disease,penetrating disease, and stricturing and penetrating disease.
 4. Themethod of claim 1, provided a SNP at rs9355610 is detected in the sampleobtained from the subject.
 5. The method of claim 4, wherein the SNP atrs9355610 comprises a “G” allele at nucleoposition 501 within SEQ ID NO:3.
 6. The method of claim 1, provided a SNP at rs6478109 or a SNP atrs7848647, or a combination thereof, is detected in the sample obtainedfrom the subject.
 7. The method of claim 1, wherein the therapeuticagent comprises an anti-Tumor Necrosis Factor Ligand 1 (TL1A) antibody.8. The method of claim 1, wherein the IBD is Crohn's disease (CD),ulcerative colitis (UC), medically refractory UC (mrUC), or acombination thereof.
 9. A method of diagnosing and treating inflammatorybowel disease in a subject, the method comprising: a) subjecting asample obtained from the subject to an assay adapted to determine apresence or an absence of a genotype comprising a single nucleotidepolymorphism (SNP) rs2149092 comprising a “T” at a nucleoposition 501within SEQ ID NO: 2; b) detecting the presence or the absence of thegenotype; c) diagnosing inflammatory bowel disease (IBD) in the subjectwhen the presence of the genotype is detected in step (b); and d)treating the IBD in the subject diagnosed in (c) by administering aneffective amount of a therapeutic agent to the subject.
 10. The methodof claim 9, wherein the genotype further comprises a SNP at rs1819333comprising an “A” allele at a nucleoposition 501 within SEQ ID NO: 1.11. The method of claim 9, wherein the IBD is severe IBD characterizedby at least one of a therapeutic failure of an anti-Tumor NecrosisFactor alpha (TNFa) therapy, multiple flare-ups per year, stricturingdisease, penetrating disease, and stricturing and penetrating disease.12. The method of claim 9, provided the genotype further comprises a SNPat rs9355610 comprising a “G” allele at nucleoposition 501 within SEQ IDNO:
 3. 13. The method of claim 9, wherein the assay comprises agenotyping assay selected from the group consisting of quantitativepolymerase chain reaction (qPCR), a single nucleotide polymorphism (SNP)array, and sequencing.
 14. The method of claim 9, provided the genotypefurther comprises at least one of a SNP at rs6478109 and a SNP atrs7848647.
 15. The method of claim 9, wherein the therapeutic agentcomprises an anti-Tumor Necrosis Factor Ligand 1 (TL1A) antibody. 16.The method of claim 9, wherein the IBD is Crohn's disease, ulcerativecolitis (UC), medically refractory UC, or a combination thereof.
 17. Themethod of claim 15, wherein the anti-TL1A antibody comprises aneutralizing TL1A antibody.
 18. The method of claim 7, wherein theanti-TL1A antibody comprises a neutralizing TL1A antibody.